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Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods. 2016 Jun;13(6):521-7. doi: 10.1038/nmeth.3853. Epub 2016 May 2. PubMed PMID: 27135972; PubMed Central PMCID: PMC4887336.
Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS. A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. J Am Soc Nephrol. 2016 Apr;27(4):1015-28. doi: 10.1681/ASN.2015010060. Epub 2015 Aug 10. PubMed PMID: 26260164; PubMed Central PMCID: PMC4814182.
Roux J, Hafner M, Bandara S, Sims JJ, Hudson H, Chai D, Sorger PK. Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold. Mol Syst Biol. 2015 May 7;11(5):803. doi: 10.15252/msb.20145584. PubMed PMID: 25953765; PubMed Central PMCID: PMC4461398.
Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W449-60. doi: 10.1093/nar/gku476. Epub 2014 Jun 6. PubMed PMID: 24906883; PubMed Central PMCID: PMC4086130.
Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Muhlich JL, Schoeberl B, Sorger PK. Analysis of growth factor signaling in genetically diverse breast cancer lines. BMC Biol. 2014 Mar 21;12:20. doi: 10.1186/1741-7007-12-20. PubMed PMID: 24655548; PubMed Central PMCID: PMC4234128.
Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Schoeberl B, Sorger PK. Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines. Sci Signal. 2013 Sep 24;6(294):ra84. doi: 10.1126/scisignal.2004379. PubMed PMID: 24065145; PubMed Central PMCID: PMC3845839.
Koeppl H, Hafner M, Lu J. Mapping behavioral specifications to model parameters in synthetic biology. BMC Bioinformatics. 2013;14 Suppl 10:S9. doi: 10.1186/1471-2105-14-S10-S9. Epub 2013 Aug 12. PubMed PMID: 24267662; PubMed Central PMCID: PMC3750501.
Miller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity. PLoS Comput Biol. 2012;8(7):e1002579. doi: 10.1371/journal.pcbi.1002579. Epub 2012 Jul 19. PubMed PMID: 22829755; PubMed Central PMCID: PMC3400602.
De Los Rios P, Hafner M, Pastore A. Explaining the length threshold of polyglutamine aggregation. J Phys Condens Matter. 2012 Jun 20;24(24):244105. doi: 10.1088/0953-8984/24/24/244105. Epub 2012 May 18. PubMed PMID: 22595533.
Hafner M, Koeppl H, Gonze D. Effect of network architecture on synchronization and entrainment properties of the circadian oscillations in the suprachiasmatic nucleus. PLoS Comput Biol. 2012;8(3):e1002419. doi: 10.1371/journal.pcbi.1002419. Epub 2012 Mar 8. PubMed PMID: 22423219; PubMed Central PMCID: PMC3297560.
Hafner M, Koeppl H. Stochastic Simulations in Systems Biology . In: Handbook of Research on Computational Science and Engineering: Theory and Practice. Leng J, Sharrock W, editors. Hershey, PA: IGI Global; 2012.
Koeppl H, Hafner M, Ganguly A, Mehrotra A. Deterministic characterization of phase noise in biomolecular oscillators. Phys Biol. 2011 Oct;8(5):055008. doi: 10.1088/1478-3975/8/5/055008. Epub 2011 Aug 10. PubMed PMID: 21832803.
Zamora-Sillero E, Hafner M, Ibig A, Stelling J, Wagner A. Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Syst Biol. 2011 Sep 15;5:142. doi: 10.1186/1752-0509-5-142. PubMed PMID: 21920040; PubMed Central PMCID: PMC3201035.
Hafner M, Petrov T, Lu J, Koeppl H. Rational design of robust biomolecular circuits: from specification to parameters . In: Design and Analysis of Bio-Molecular Circuits. Koeppl H, Densmore D, di Bernardo M, Setti G, editors. New York: Springer; 2011.
Gonze D, Hafner M. Positive Feedbacks Contribute to the Robustness of the Cell Cycle with Respect to Molecular Noise . In: Advances in the Theory of Control, Signals and Systems with Physical Modeling. Levine J, Mullhaupt P, editors. Heidelberg: Springer-Verlag Berlin Heidelberg; 2011. p.283-295.
Hafner M, Koeppl H, Hasler M, Wagner A. 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Comput Biol. 2009 Oct;5(10):e1000534. doi: 10.1371/journal.pcbi.1000534. Epub 2009 Oct 16. PubMed PMID: 19834597; PubMed Central PMCID: PMC2758577.
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