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Naz M, Kodamullil AT, Hofmann-Apitius M. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Brief Bioinform. 2015. URL:

Boué S, Talikka M, Westra JW, Hayes W, Di Fabio A, Park J, Schlage WK, Sewer A, Fields B, Ansari S, Martin F, Veljkovic E, Kenney R, Peitsch MC, Hoeng J. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Database. 2015. Apr 17;2015. URL:

Kodamullil AT, Younesi E, Naz M, Bagewadi S, Hofmann-Apitius M. Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysisAlzheimers Dement. 2015 Apr 4. pii: S1552-5260(15)00083-7.

sbv IMPROVER Project Team, Binder J, Boue S, Di Fabio A, Fields RB, Hayes W, Hoeng J, Park JS, Peitsch MC. Reputation-based collaborative network biology. Pac Symp Biocomput. 2015:270-81. URL:


Slater T. Recent advances in modeling languages for pathway maps and computable biological networks. Drug Discovery Today. 2014. 19:193-8. PMID: 24444544.

Vasilyev DM, Thomson TM, Frushour BP, Martin F, Sewer A. An algorithm for score aggregation over causal biological networks based on random walk sampling. BMC Res Notes. 2014 7:516. URL:


Catlett NL, Bargnesi AJ, Ungerer S, Seagaran T., Ladd W, Elliston KO, Pratt D. Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. BMC Bioinformatics 2013, 14:340. URL:

Laifenfeld D, Luing Q, Swiss R, Park J, Macoritto M, Will Y, Younis H, Lawton M. Utilization of Reverse Causal Reasoning of Hepatic Gene Expression in Rats to Identify Molecular Pathways of Idiosyncratic Drug-Induced Liver Injury. Toxicol Sci. 2013 Oct 17. PMID: 24136188.

sbv IMPROVER project team (in alphabetical order), Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B, Peitsch MC, Poussin C, Pratt D, Rhrissorrakrai K, Schlage WK, Stolovitzky G, Talikka M. On Crowd-verification of Biological Networks. Bioinform Biol Insights. 2013 Oct 10;7:307-25. doi: 10.4137/BBI.S12932. PMID: 24151423.

Thomson TM, Sewer A, Martin F, Belcastro V, Frushour BP, Gebel S, Park J, Schlage WK, Talikka M, Vasilyev DM, Westra JW, Hoeng J, Peitsch MC. Quantitative assessment of biological impact using transcriptomic data and mechanistic network models.  Toxicol Appl Pharmacol. 2013 Aug 8;272(3):863-878. PMID: 23933166.

Belcastro V, Poussin C, Gebel S, Mathis C, Schlage WK, Lichtner RB, Quadt-Humme S, Wagner S, Hoeng J, Peitsch MC. Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset. Bioinform Biol Insights. 2013 Jul 23;7:217-30. PMID: 23926424; PubMed Central PMCID: PMC3733638.

Westra JW, Schlage WK, Hengstermann A, Gebel S, Mathis C, Thomson T, Wong B, Hoang V, Veljkovic E, Peck M, Lichtner RB, Weisensee D, Talikka M, Deehan R, Hoeng J, Peitsch MC. A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue. Bioinform Biol Insights. 2013 Jun 20;7:167-92. PMID: 23843693; PubMed Central PMCID: PMC3700945.

Gebel S, Lichtner RB, Frushour B, Schlage WK, Hoang V, Talikka M, Hengstermann A, Mathis C, Veljkovic E, Peck M, Peitsch MC, Deehan R, Hoeng J, Westra JW. Construction of a computable network model for DNA damage, autophagy, cell death, and senescence. Bioinform Biol Insights. 2013;7:97-117.  PMID: 23515068; PubMed Central PMCID: PMC3596057.

O'Connor MA, Koza-Taylor P, Campion SN, Aleksunes LM, Gu X, Enayetallah AE, Lawton MP, Manautou JE. Analysis of Changes in Hepatic Gene Expression in a Murine Model of Tolerance to Acetaminophen Hepatotoxicity (Autoprotection). Toxicol Appl Pharmacol. 2013 Oct 11. PMID: 24126418.

Enayetallah AE, Puppala D, Ziemek D, Fischer JE, Kantesaria S, Pletcher MT. Assessing the translatability of In vivo cardiotoxicity mechanisms to In vitro models using causal reasoning. BMC Pharmacol Toxicol. 2013 Sep 6;14(1):46. PMID: 24010585.

Park JS, Schlage WK, Frushour BP, Talikka M, et al. Construction of a Computable Network Model of Tissue Repair and Angiogenesis in the Lung. J Clinic Toxicol S12:002. doi: 10.4172/2161-0495.S12-002. URL:



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. Comparative transcriptional network modeling of three PPAR-α/γ co-agonists reveals distinct metabolic gene signatures in primary human hepatocytes. PLoS One. 2012;7(4):e35012. PMID: 22514701; PubMed Central PMCID: PMC3325914.

Laifenfeld D, Drubin DA, Catlett NL, Park JS, Van Hooser AA, Frushour BP, de Graaf D, Fryburg DA, Deehan R. Early patient stratification and predictive biomarkers in drug discovery and development: a case study of ulcerative colitis anti-TNF therapy. Adv Exp Med Biol. 2012;736:645-53. PMID: 22161357.

Toedter G, Li K, Sague S, Ma K, Marano C, Macoritto M, Park J, Deehan R, Matthews A, Wu GD, Lewis JD, Arijs I, Rutgeerts P, Baribaud F. Genes associated with intestinal permeability in ulcerative colitis: changes in expression following infliximab therapy. Inflamm Bowel Dis. 2012 Aug;18(8):1399-410. PMID: 22223479.

Martin F, Thomson TM, Sewer A, Drubin DA, Mathis C, Weisensee D, Pratt D, Hoeng J, Peitsch MC. Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. BMC Syst Biol. 2012 May 31;6:54. PMID: 22651900; PubMed Central PMCID: PMC3433335.

Hoeng J, Deehan R, Pratt D, Martin F, Sewer A, Thomson TM, Drubin DA, Waters CA, de Graaf D, Peitsch MC. A network-based approach to quantifying the impact of biologically active substances. Drug Discov Today. 2012 May;17(9-10):413-8. doi:10.1016/j.drudis.2011.11.008. Epub 2011 Dec 2. PubMed PMID: 22155224.


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. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. BMC Syst Biol. 2011 Oct 19;5:168. PMID: 22011616; PubMed Central PMCID: PMC3224482.

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. Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst Biol. 2011 Jul 2;5:105. PMID: 21722388; PubMed Central PMCID: PMC3160372.


Kumar R, Blakemore SJ, Ellis CE, Petricoin EF 3rd, Pratt D, Macoritto M, Matthews AL, Loureiro JJ, Elliston K. Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693. BMC Genomics. 2010 Jul 6;11:419. PMID: 20604938; PubMed Central PMCID: PMC2996947.

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. The role of hypoxia in 2-butoxyethanol-induced hemangiosarcoma. Toxicol Sci. 2010 Jan;113(1):254-66. PMID: 19812364; PubMed Central PMCID: PMC2794330.


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. Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo. BMC Syst Biol. 2009 Mar 10;3:31. PMID: 19284563; PubMed Central PMCID: PMC2660283.

Blander G, Bhimavarapu A, Mammone T, Maes D, Elliston K, Reich C, Matsui MS, Guarente L, Loureiro JJ. SIRT1 promotes differentiation of normal human keratinocytes. J Invest Dermatol. 2009 Jan;129(1):41-9. PMID: 18563176; PubMed Central PMCID: PMC3526938.

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