Publications

2012

Zhao S, Iyengar R. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol. 2012 Feb 10;52:505-21.
PMID: 22235860 | EndNote Citation

Rozenfeld R, Bushlin I, Gomes I, Tzavaras N, Gupta A, Neves S, Battini L, Gusella GL, Lachmann A, Ma'ayan A, Blitzer RD, Devi LA. Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons. PLoS One. 2012;7(1):e29239.
PMID: 22235275 | PMCID: PMC3250422 | EndNote Citation

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma'ayan A Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers. Bioinformatics. 2012 Jan 1;28(1):105-11.
PMID: 22080467 | EndNote Citation

2011

Mazloom AR, Dannenfelser R, Clark NR, Grigoryan AV, Linder KM, Cardozo TJ, Bond JC, Boran ADW, Iyengar R, Malovannaya A, Lanz RB, Ma'ayan A Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comput Biol. 7(12): e1002319.
PMID: 22219718 | EndNote Citation

Xu H, Ma'ayan A Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. Lect Notes Comput Sci. 2011;7058:15-22.
PMID: 22180699 | EndNote Citation

Abul-Husn NS, Annangudi SP, Ma'ayan A, Ramos-Ortolaza DL, Stockton SD Jr, Gomes I, Sweedler JV, Devi LA Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis. PLoS One. 2011;6(10):e25535.
PMID: 22043286 | PMCID: PMC3197197 | EndNote Citation

Baroukh C, Jenkins SL, Danenfelser R, Ma'ayan A. Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol Med. 2011 Oct 13;6(1):15.
PMID: 21995939 | EndNote Citation

Sirovich L. Probabilistic reasoning in data analysis. Sci Signal. 2011 Sep 27;4(192):tr14.
PMID: 21954295 | EndNote Citation

Hayot F. Simulations of stochastic biological phenomena. Sci Signal. 2011 Sep 27;4(192):tr13.
PMID: 21954294 | EndNote Citation

Neves SR. Developing Models in Virtual Cell Sci Signal. 2011 Sep 27;4(192):tr12.
PMID: 21954293 | EndNote Citation

Sobie EA. Computational Modeling of the Cell Cycle Sci Signal. 2011 Sep 27;4(192):tr11.
PMID: 21954292 | EndNote Citation

Sobie EA. Bistability in Biochemical Signaling Models Sci Signal. 2011 Sep 27;4(192):tr10.
PMID: 21954291 | EndNote Citation

Costa KD, Kleinstein SH, Hershberg U. Biomedical model fitting and error analysis. Sci Signal. 2011 Sep 27;4(192):tr9.
PMID: 21954296 | EndNote Citation

Neves SR. Obtaining and estimating kinetic parameters from the literature. Sci Signal. 2011 Sep 20;4(191):tr8.
PMID: 21934111 | EndNote Citation

Sobie EA. An Introduction to MATLAB. Sci Signal. 2011 Sep 20;4(191):tr7.
PMID: 21934110 | EndNote Citation

Sobie EA. An introduction to dynamical systems. Sci Signal. 2011 Sep 20;4(191):tr6.
PMID:21934109 | EndNote Citation

Ma'ayan A. Introduction to network analysis in systems biology. Sci Signal. 2011 Sep 13;4(190):tr5.
PMID: 21917719 | EndNote Citation

Clark NR, Ma'ayan A. Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis. Sci Signal. 2011 Sep 13;4(190):tr4.
PMID: 21917718 | EndNote Citation

Clark NR, Ma'ayan A. Introduction to statistical methods to analyze large data sets: principal components analysis. Sci Signal. 2011 Sep 13;4(190):tr3.
PMID: 21917717 | EndNote Citation

Sobie EA, Lee YS, Jenkins SL, Iyengar R. Systems biology--biomedical modeling. Sci Signal. 2011 Sep 13;4(190):tr2
PMID: 21917716 | EndNote Citation

Miller LK, Devi LA. The highs and lows of cannabinoid receptor expression in disease: mechanisms and their therapeutic implications. Pharmacol Rev. 2011 Sep;63(3):461-70.
PMID: 21752875 | PMCID: PMC3141881 | EndNote Citation

Ramay HR, Liu OZ, Sobie EA. Recovery of cardiac calcium release is controlled by sarcoplasmic reticulum refilling and ryanodine receptor sensitivity. Cardiovasc Res. 2011 Sep 1;91(4):598-605.
PMID: 21613275 | PMCID: PMC3156908 | EndNote Citation

He JC, Chuang PY, Ma'ayan A, Iyengar R. Systems biology of kidney diseases. Kidney Int. 2011 Aug 31.
PMID: 21881558 | EndNote Citation

Crumiller M, Knight B, Yu Y, Kaplan E. Estimating the amount of information conveyed by a population of neurons. Source Front Neurosci. 2011;5:90.
PMID: 21811435 | PMCID: PMC3139929 | | EndNote Citation

Jia Z, Valiunas V, Lu Z, Bien H, Liu H, Wang HZ, Rosati B, Brink PR, Cohen IS, Entcheva E. Stimulating Cardiac Muscle by Light: Cardiac Optogenetics by Cell Delivery. Circ Arrhythm Electrophysiol. 2011 Aug 9.
PMID: 21828312 | EndNote Citation

Sirovich L, Knight B. Spiking neurons and the first passage problem. Neural Comput. 2011 Jul;23(7):1675-703.
PMID: 21492014 | EndNote Citation

Neves SR. Modeling of spatially-restricted intracellular signaling. Wiley Interdiscip Rev Syst Biol Med. 2011 Jul 15.
PMID: 21766466 | EndNote Citation

Liu J, Fackelmayer OJ, Hicks DB, Preiss L, Meier T, Sobie EA, Krulwich TA. Mutations in a Helix-1 Motif of the ATP Synthase c-Subunit of Bacillus pseudofirmus OF4 Cause Functional Deficits and Changes in the c-Ring Stability and Mobility on Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis. Biochemistry. 2011 Jun 21;50(24):5497-506.
PMID: 21568349 | PMCID: PMC3115392 | EndNote Citation

Sarkar AX, Sobie EA. Quantification of repolarization reserve to understand interpatient variability in the response to proarrhythmic drugs: A computational analysis. Heart Rhythm. 2011 Jun 7.
PMID: 21699863 | EndNote Citation

Bhalla US. Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural Netw. 2011 May 10.
PMID: 21616637 | EndNote Citation

Rozenfeld R, Gupta A, Gagnidze K, Lim MP, Gomes I, Lee-Ramos D, Nieto N, Devi LA. AT1R-CB1R heteromerization reveals a new mechanism for the pathogenic properties of angiotensin II. EMBO J. 2011 May 3;30(12):2350-63.
PMID: 21540834 | PMCID: PMC3116274 | EndNote Citation

Dannenfelser R, Lachmann A, Szenk M, Ma'ayan A. FNV: Light-weight Flash-based network and pathway viewer. Bioinformatics. 2011 Apr 15;27(8):1181-2.
PMID: 21349871 | PMCID: PMC3072557 | EndNote Citation | Biositemaps (RDF)


Leigh SY, Tattu A, Mitchell JS, Entcheva E. M3: Microscope-based maskless micropatterning with dry film photoresist. Biomed Microdevices. 2011 Apr;13(2):375-81.
PMID: 21190086 | EndNote Citation

Golebiewska U, Johnston JM, Devi L, Filizola M, Scarlata S. Differential response to morphine of the oligomeric state of μ-opioid in the presence of δ-opioid receptors. Biochemistry. 2011 Apr 12;50(14):2829-37.
PMID: 21361347 | PMCID: PMC3048119 | EndNote Citation

Guo Y, Golebiewska U, Scarlata S. Modulation of Ca2+ activity in cardiomyocytes through caveolae-Gαq interactions. Biophys J. 2011 Apr 6;100(7):1599-607.
PMID: 21463572 | PMCID: PMC3072606 | EndNote Citation

Webb RL, Ma’ayan A. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol Med. 2011 Mar 21;6(1):5.
PMID: 21418653 | PMCID: PMC3071313 | Biositemaps (RDF)

Isaacson SA, McQueen DM, Peskin CS. The influence of volume exclusion by chromatin on the time required to find specific DNA binding sites by diffusion. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3815-20.
PMID: 21300894 | PMCID: PMC3048119 | EndNote Citation

Chung CY, Bien H, Sobie EA, Dasari V, McKinnon D, Rosati B, Entcheva E. Hypertrophic phenotype in cardiac cell assemblies solely by structural cues and ensuing self-organization. FASEB J. 2011 Mar;25(3):851-62.
PMID: 21084696 | PMCID: PMC3042840 | EndNote Citation

Rangamani P, Fardin MA, Xiong Y, Lipshtat A, Rossier O, Sheetz MP, Iyengar R. Signaling network triggers and membrane physical properties control the actin cytoskeleton-driven isotropic phase of cell spreading. Biophys J. 2011 Feb 16;100(4):845-57.
PMID: 21320428 | PMCID: PMC3037558 | EndNote Citation

2010

Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol. 2010 Dec 21;4(1):173.
PMID: 21176149 | PMCID: PMC3019180 | EndNote Citation

Rozenfeld R, Devi LA. Exploring a role for heteromerization in GPCR signalling specificity. Biochem J. 2010 Dec 15;433(1):11-8.
PMID: 21158738 | PMCID: PMC3115900 | EndNote Citation

Gomes I, Dale CS, Casten K, Geigner MA, Gozzo FC, Ferro ES, Heimann AS, Devi LA. Hemoglobin-derived peptides as novel type of bioactive signaling molecules. AAPS J. 2010 Dec;12(4):658-69.
PMID: 20811967 | PMCID: PMC2976993 | EndNote Citation

Xu H, Schaniel C, Lemischka IR, Ma'ayan A. Towards a complete in-silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med. 2010 Nov-Dec;2(6):708-33.
PMID: 20890967 | PMCID: PMC2951283 | EndNote Citation

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 Oct 1;26(19):2438-44.
PMID: 20709693 | PMCID: PMC2944209 | EndNote Citation

Sarkar AX, Sobie EA. Regression analysis for constraining free parameters in electrophysiological models of cardiac cells. PLoS Comput Biol. 2010 Sep 2;6(9):e1000914. PMID: 20824123 | PMCID: PMC2932676 | EndNote Citation

Cecchi GA, Rao AR, Xiao Y, Kaplan E. Statistics of natural scenes and cortical color processing. J Vis. 2010 Sep 1;10(11):21.
PMID: 20884516 | EndNote Citation

Berger SI, Iyengar R. Role of systems pharmacology in understanding drug adverse events. Wiley Interdiscip Rev Syst Biol Med. 2010 Aug 27
PMID: 20803507 | PMCID: PMC3057924 | EndNote Citation

Babadi B, Casti A, Xiao Y, Kaplan E, Paninski L. A generalized linear model of the impact of direct and indirect inputs to the lateral geniculate nucleus. J Vis. 2010 Aug 24;10(10):22.
PMID: 20884487 | EndNote Citation

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 24;107(34):15299-304.
PMID: 20686112 | PMCID: PMC2930550 | EndNote Citation

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.
PMID: 20703299 | PMCID: PMC3146551 | EndNote Citation

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. PMID: 20689804 | PMCID: PMC2914638 | EndNote Citation

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. PMID: 20687179 | PMCID: PMC2927836 | EndNote Citation

Boran AD, Iyengar R. Systems pharmacology. Mt Sinai J Med. 2010 Jul-Aug;77(4):333-44.
PMID: 20687178 | PMCID: PMC3113679 | EndNote Citation

Hipser C, Bushlin I, Gupta A, Gomes I, Devi LA. Role of antibodies in developing drugs that target G-protein-coupled receptor dimers. Mt Sinai J Med. 2010 Jul-Aug;77(4):374-80.
PMID: 20687183 | PMCID: PMC2917817 | EndNote Citation

Iyengar R. Drug discovery in academic settings. Mt Sinai J Med. 2010 Jul-Aug;77(4):325-6.
PMID: 20687176 | EndNote Citation

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.
PMID: 20647592 | PMCID: PMC3125674 | EndNote Citation

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.
PMID: 20562890 | PMCID: PMC3037798 | EndNote Citation

Lee P, Griffith BE, Peskin CS. The immersed boundary method for advection-electrodiffusion with implicit timestepping and local mesh refinement. J Comput Phys. 2010 Jul 1;229(13):5208-5227.
PMID: 20454540 | PMCID: PMC2864960

Ramay HR, Jafri MS, Lederer WJ, Sobie EA. Predicting local SR Ca(2+) dynamics during Ca(2+) wave propagation in ventricular myocytes. Biophys J. 2010 Jun 2;98(11):2515-23.
PMID: 20513395 | PMCID: PMC2877363 | EndNote Citation

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.
PMID: 20483321 | PMCID:PMC2872297 | EndNote Citation

Boran AD, Iyengar R. Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Discov Devel. 2010 May;13(3):297-309.
PMID: 20443163 | PMCID: PMC3068535 | EndNote Citation

Hardy S and Iyengar R. 2010. Analysis of dynamical models of signaling networks with Petri nets and dynamic graphs. Modeling in Systems Biology, Computational Biology, 2011, Volume 16, Part 3, 225-251.

Krulwich TA, Liu J, Morino M, Fujisawa M, Ito M, Hicks DB. 2010. Adaptive mechanisms of extreme alkaliphiles. Extremophiles Handbook.
Horikoshi K, Antranikian G, Bull AT, Robb FT, Stetter KO. (Eds.).

Yu Y, Crumiller M, Knight B, Kaplan E Estimating the amount of information carried by a neuronal population. Front Comput Neurosci. 2010 Apr 26;4:10.
PMID: 20461228 | PMCID: PMC2866452 | EndNote Citation

Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Sci Signal. 2010 Apr 20;3(118):ra30.
PMID: 20407125 | PMCID: PMC3068558 | EndNote Citation

MacArthur BD, Sanchez-Garcia RJ, Ma'ayan A. Microdynamics and criticality of adaptive regulatory networks. Phys Rev Lett. 2010 Apr 23;104(16):168701.
PMID: 20482087 | PMCID: PMC2925242 | Abstract | EndNote Citation

Yamada YR, Peskin CS. The influence of look-ahead on the error rate of transcription. Math. Mod. Nat. Phen. 2010 Apr; 5(3): 206-227.
PMID: 22162915 | PMCID: PMC3235181

Golebiewska U, Scarlata S. The effect of membrane domains on the G protein-phospholipase Cbeta signaling pathway. Crit Rev Biochem Mol Biol. 2010 Apr;45(2):97-105.
PMID: 20128735 | PMCID: PMC2857923

Rozenfeld R, Devi LA. Receptor heteromerization and drug discovery. Trends Pharmacol Sci. 2010 Mar;31(3):124-30.
PMID: 20060175 | PMCID: PMC2834828 | EndNote Citation

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.
PMID: 20207949 | PMCID: PMC2851797 | EndNote Citation

Sirovich L, Stoeckle MY, Zhang Y. Structural analysis of biodiversity. PLoS One. 2010 Feb 24;5(2):e9266.
PMID: 20195371 | PMCID: PMC2827552 | EndNote Citation

Lachmann A, Ma'ayan A. Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics. 2010 Feb 12;11(1):87.
PMID: 20152038 | PMCID: PMC2843617 | EndNote Citation | Biositemaps (RDF)

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.
PMID: 19695992 | PMCID: PMC3153073 | EndNote Citation

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. 2010 Jan 19;107(3):1247-52.
PMID: 20080566 | PMCID: PMC2824311 | EndNote Citation

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.
PMID: 19861414 | PMCID: PMC2801262 | EndNote Citation

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.
PMID: 19892805 | PMCID: PMC2796822 | EndNote Citation | Biositemaps (RDF)

2009

Isaacson SA, Isaacson D. Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials. Rev E Stat Nonlin Soft Matter Phys. 2009 Dec;80(6 Pt 2):066106.
PMID:20365230 | EndNote Citation

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.
PMID:19924215 | EndNote Citation

Berger SI, Iyengar R. Network analyses in systems pharmacology. Bioinformatics. 2009 Oct 1;25(19):2466-72.
PMID:19648136 | PMCID: PMC2752618 | EndNote Citation

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.
PMID:19738627 | PMCID: PMC2928569 | EndNote Citation

Sirovich L, Stoeckle MY, Zhang Y. A scalable method for analysis and display of DNA sequences. PLoS One. 2009 Oct 2;4(10):e7051.
PMID:19798412 | PMCID: PMC2749217 | EndNote Citation | Biositemaps (RDF)

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.
PMID: 19684605 | PMCID: PMC2765465 | EndNote Citation

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.
PMID: 19380512 | PMCID: PMC2735371 | EndNote Citation

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.
PMID: 19562802 | PMCID: PMC2766278 | EndNote Citation | Biositemaps (RDF)

Sirovich L, Meytlis M. Symmetry, probability, and recognition in face space. Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):6895-9.
PMID:19365075 | PMCID: PMC2678476 | EndNote Citation

Yamada YR, Peskin CS. A look-ahead model for the elongation dynamics of transcription. Biophys J. 2009 Apr 22;96(8):3015-31.
PMID: 19383448 | PMCID: PMC2718317 | EndNote Citation

Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics. 2009 Mar 1;25(5):684-6.
PMID:19176546 | PMCID: PMC2647829 | EndNote Citation | Biositemaps (RDF)

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.
PMID: 18940806 | PMCID: PMC2645810 | EndNote Citation

Neves SR, Iyengar R. Models of spatially restricted biochemical reaction systems. J Biol Chem. 2009 Feb 27;284(9):5445-9.
PMID: 18940805 | PMCID: PMC2645809 | EndNote Citation

Iyengar R. Computational biochemistry: Systems biology minireview series. J Biol Chem. 2009 Feb 27;284(9):5425-6.
PMID: 18940804 | EndNote Citation

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.
PMID: 18977767 | PMCID:PMC2639131 | EndNote Citation

Sobie EA. Parameter sensitivity analysis in electrophysiological models using multivariable regression. Biophys J. 2009 Feb 18;96(4):1264-74.
PMID: 19217846 | PMCID: PMC2717232 | EndNote Citation

Wist AD, Berger SI, Iyengar R. Systems pharmacology and genome medicine: a future perspective. Genome Med. 2009 Jan 22;1(1):11.
PMID: 19348698 | PMCID: PMC2651594 | EndNote Citation

Ma'ayan A, Jenkins SL, Barash A, Iyengar R Neuro2A differentiation by Galphai/o pathway. Sci Signal. 2009 Jan 20;2(54):cm1.
PMID: 19155528 | PMCID: PMC2649824 | EndNote Citation

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.
PMID: 19154595 | PMCID: PMC2637233 | EndNote Citation | Biositemaps (RDF)

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.

2008

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.
PMID: 19329576 | PMCID: PMC2738746 | EndNote Citation

Ray S, Bhalla US. PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinformatics. 2008;2:6. Epub 2008 Dec 19.
PMID: 19129924 | PMCID: PMC2614320 | EndNote Citation | Biositemaps (RDF)

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.
PMID: 19033453 | PMCID: PMC2614745 | EndNote Citation

Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol. 2008 Sep;2(5):206-21.
PMID: 19045817 | PMCID: PMC2745214 | EndNote Citation

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.
PMID: 18537452 | PMCID: PMC2453221 | EndNote Citation

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.
PMID: 18487186 | PMCID: PMC2776723 | EndNote Citation

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.
PMID: 18485874 | PMCID: PMC2728678 | EndNote Citation

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.
PMID: 19162616 | PMCID: PMC3153068 | EndNote Citation

Royer CA, Scarlata SF. Fluorescence approaches to quantifying biomolecular interactions. Methods Enzymol. 2008;450:79-106.
PMID: 19152857 | EndNote Citation

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