Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A. ChEA: Transcription Factor Regulation Inferred from Integrating Genome-Wide ChIP-X Experiments. Bioinformatics. 2010 Aug 13.

Méndez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, Ma'ayan A, Enikolopov GN, Frenette PS. Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Nature. 2010 Aug 12;466(7308):829-34

Ma'ayan A, He JC. Protein kinase target discovery from genome-wide messenger RNA expression profiling. Mt Sinai J Med. 2010 Jul-Aug;77(4):345-9.

Xiao K, Sun J, Kim J, Rajagopal S, Zhai B, Villén J, Haas W, Kovacs JJ, Shukla AK, Hara MR, Hernandez M, Lachmann A, Zhao S, Lin Y, Cheng Y, Mizuno K, Ma'ayan A, Gygi SP, Lefkowitz RJ. Global phosphorylation analysis of {beta}-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR). Proc Natl Acad Sci U S A. 2010 Aug 4.

Preiss L, Yildiz O, Hicks DB, Krulwich TA, Meier T. A new type of proton coordination in an F(1)F(o)-ATP synthase rotor ring. PLoS Biol. 2010 Aug 3;8(8):e1000443.

Gupta A, Mulder J, Gomes I, Rozenfeld R, Bushlin I, Ong E, Lim M, Maillet E, Junek M, Cahill CM, Harkany T, Devi LA. Increased abundance of opioid receptor heteromers after chronic morphine administration. Sci Signal. 2010 Jul 20;3(131):ra54.

Sobie EA, Jenkins SL, Iyengar R, Krulwich TA. 2010. Training in systems pharmacology: Pre-doctoral program in pharmacology and systems biology at Mount Sinai School of Medicine. Clin Pharmacol Ther. 2010 Jul;88(1):19-22.

Xiong Y, Rangamani P, Fardin MA, Lipshtat A, Dubin-Thaler B, Rossier O, Sheetz MP, Iyengar R. Mechanisms controlling cell size and shape during isotropic cell-spreading. Biophys J. 2010 May 19;98(10):2136-46.

Hardy S and Iyengar R. 2010. Analysis of dynamical models of signaling networks with Petri nets and dynamic graphs, in Modeling in Systems Biology: The Petri Net Approach, Springer, In Press.

Krulwich TA, Liu J, Morino M, Fujisawa M, Ito M, Hicks DB. 2010. Adaptive mechanisms of extreme alkaliphiles. In: Extremophiles Handbook. Horikoshi, K., Antranikian, G., Bull, A., Robb, F., Stetter, K. (eds), Springer, Heidelberg, In Press.

Berger SI, Ma'ayan A, Iyengar R. 2010. Systems pharmacology of arrhythmias. Sci Signal. 2010 Apr 20;3(118):ra30.

MacArthur BD, Sanchez-Garcia RJ, Ma'ayan A. Microdynamics and criticality of adaptive regulatory networks. Phys Rev Lett. 2010 Apr 23;104(16):168701.
Abstract»

Xu H, Schaniel C, Lemischka IR, Ma'ayan A. Towards a complete in-silico, multi-layered embryonic stem cell regulatory network. Systems Biology and Medicine, Published Online: Mar 24 2010

Rodriguez-Brenes IA, Peskin CS. Quantitative theory of telomere length regulation and cellular senescence. Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5387-92.
PNAS Article»

Sirovich L, Stoeckle MY, Zhang Y. Structural analysis of biodiversity. PLoS One. 2010 Feb 24;5(2):e9266.

Lachmann A, Ma'ayan A. Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics. 2010 Feb 12;11(1):87.

Jia Z, Bien H, Entcheva E. Detecting space-time alternating biological signals close to the bifurcation point. Trans Biomed Eng. 2010 Feb;57(2):316-24.

Zorina Y, Iyengar R, Bromberg KD. Cannabinoid 1 receptor and interleukin-6 receptor together induce integration of protein kinase and transcription factor signaling to trigger neurite outgrowth. J Biol Chem. 2010 Jan 8;285(2):1358-70.

Rozenfeld R, Devi LA. Receptor heteromerization and drug discovery. Trends Pharmacol Sci. 2010 Jan 6.

MacArthur BD, Lachmann A, Lemischka IR, Ma'ayan A. GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinformatics. 2010 Jan 1;26(1):143-4.

Lipshtat A, Jayaraman G, He JC, Iyengar R. Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues. Proc Natl Acad Sci U S A. 2009 Dec 28.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR. Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature. 2009 Nov 19;462(7271):358-62.

Berger SI, Iyengar R. Network analyses in systems pharmacology. Bioinformatics. 2009 Oct 1;25(19):2466-72.

Macarthur BD, Ma'ayan A, Lemischka IR. Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol. 2009 Oct;10(10):672-81.

Sirovich L, Stoeckle MY, Zhang Y. A scalable method for analysis and display of DNA sequences. PLoS One. 2009 Oct 2;4(10):e7051.

Cordeddu V, Di Schiavi E, Pennacchio LA, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, Flex E, Lepri F, Bartholdi D, Kutsche K, Ferrero GB, Anichini C, Selicorni A, Rossi C, Tenconi R, Zenker M, Merlo D, Dallapiccola B, Iyengar R, Bazzicalupo P, Gelb BD, Tartaglia M. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet. 2009 Sep;41(9):1022-6.

Gomes I, Grushko JS, Golebiewska U, Hoogendoorn S, Gupta A, Heimann AS, Ferro ES, Scarlata S, Fricker LD, Devi LA. Novel endogenous peptide agonists of cannabinoid receptors. FASEB J. 2009 Sep;23(9):3020-9.

Abul-Husn NS, Bushlin I, Morón JA, Jenkins SL, Dolios G, Wang R, Iyengar R, Ma’ayan A, Devi LA. Systems approach to explore components and interactions in the presynapse. Proteomics 2009 Jun;9(12):3003-15.

Yamada YR, Peskin CS. A look-ahead model for the elongation dynamics of transcription. Biophys J. 2009 Apr 22;96(8):3015-31.

Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics. 2009 Mar 1;25(5):684-6.

Ma'ayan A. Insights into the organization of biochemical regulatory networks using graph theory analyses. J Biol Chem. 2009 Feb 27;284(9):5451-5.

Neves SR, Iyengar R. Models of spatially restricted biochemical reaction systems. J Biol Chem. 2009 Feb 27;284(9):5445-9.

Iyengar R. Computational biochemistry: Systems biology minireview series. J Biol Chem. 2009 Feb 27;284(9):5425-6.

Protas L, Dun W, Jia Z, Lu J, Bucchi A, Kumari S, Chen M, Cohen IS, Rosen MR, Entcheva E, Robinson RB. Expression of skeletal but not cardiac Na+ channel isoform preserves normal conduction in a depolarized cardiac syncytium. Cardiovasc Res. 2009 Feb 15;81(3):528-35.

Sobie EA. Parameter sensitivity analysis in electrophysiological models using multivariable regression. Biophys J. 2009 Feb 18;96(4):1264-74.

Wist AD, Berger SI, Iyengar R. Systems pharmacology and genome medicine: a future perspective. Genome Med. 2009 Jan 22;1(1):11.

Ma'ayan A, Jenkins SL, Barash A, Iyengar R Neuro2A differentiation by Galphai/o pathway. Sci Signal. 2009 Jan 20;2(54):cm1.

Ma'ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R. SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst Biol. 2009 Jan 20;3:10.

33. Xiao Y. and Kaplan E. 2009. Information about color and orientation in the primate visual cortex In: High Throughput Image Analysis and Reconstruction/A. R. Rao and G. Cecchi, (Eds.) Artech House Publishing, Ch. 10:219-229.

MacArthur BD, Ma'ayan A, Lemischka IR. Toward stem cell systems biology: from molecules to networks and landscapes. Cold Spring Harb Symp Quant Biol. 2008;73:211-5.

Ray S, Bhalla US. PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinformatics. 2008;2:6. Epub 2008 Dec 19.

Ma'ayan A, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19235-40.

Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol. 2008 Sep;2(5):206-21.

Ma'ayan A, Lipshtat A, Iyengar R, Sontag ED. Proximity of intracellular regulatory networks to monotone systems. IET Syst Biol. 2008 May;2(3):103-12.

Bromberg KD, Ma'ayan A, Neves SR, Iyengar R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 2008;320(5878):903-9.

Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R. Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell 2008;133(4):666-80.

Jia Z, Bien H, Entcheva E. A sensitive algorithm for automatic detection of space-time alternating signals in cardiac tissue. Conf Proc IEEE Eng Med Biol Soc. 2008;2008:153-6.

Royer CA, Scarlata SF. Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol. 2008;450:79-106.