SBCNY Publications

Falkenberg CV, Azeloglu EU, Stothers M, Deerinck TJ, Chen Y, He JC, Ellisman MH, Hone JC, Iyengar R, Loew LM. Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability. PLoS Comput Biol. 2017 Mar 16;13(3):e1005433.
PMID: 28301477 | PMCID: PMC5373631 | EndNote Citation

Hu M, Azeloglu EU, Ron A, Tran-Ba KH, Calizo RC, Tavassoly I, Bhattacharya S, Jayaraman G, Chen Y, Rabinovich V, Iyengar R, Hone JC, He JC,4, Kaufman LJ. A biomimetic gelatin-based platform elicits a pro-differentiation effect on podocytes through mechanotransduction. Sci Rep. 2017 Mar 6;7:43934.
PMID: 28262745 | PMCID: PMC5338254 | EndNote Citation

Stillitano F, Hansen J, Kong CW, Karakikes I, Funck-Brentano C, Geng L, Scott S, Reynier S, Wu M, Valogne Y, Desseaux C, Salem JE, Jeziorowska D, Zahr N, Li R, Iyengar R, Hajjar RJ, Hulot JS. Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells. Elife. 2017 Jan 30;6.
PMID: 28134617 | PMCID: PMC5279943 | EndNote Citation

Bouhaddou M, Birtwistle MR. Kinetic Models of Biochemical Signaling Networks Systems Pharmacology and Pharmacodynamics, Chapter 6 (02 December 2016)

Marc R. Birtwistle, Jens Hansen, James M. Gallo, Sreeharish, Muppirisetty, Peter Man-Un Ung, Ravi Iyengar, Avner Schlessinger Systems Pharmacology: An Overview Systems Pharmacology and Pharmacodynamics, Chapter 4 (02 December 2016)

Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR. Drug response consistency in CCLE and CGP. Nature. 2016 Nov 30;540(7631):E9-E10.
PMID: 27905419 | EndNote Citation

Song RS, Tolentino R, Sobie EA, Neves-Zaph SR. Cross-regulation of Phosphodiesterase 1 and Phosphodiesterase 2 Activities Controls Dopamine-mediated Striatal α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Trafficking. J Biol Chem. 2016 Oct 28;291(44):23257-23267.
PMID: 27605670 | PMCID: PMC5087742 | EndNote Citation

Devenyi RA, Ortega FA, Groenendaal W, Krogh-Madsen T, Christini DJ2, Sobie EA. Differential roles of two delayed rectifier potassium currents in regulation of ventricular action potential duration and arrhythmia susceptibility. J Physiol. 2016 Oct 24. doi: 10.1113/JP273191
PMID: 27779762 | EndNote Citation

Mayourian J, Savizky RM, Sobie EA, Costa KD Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes. PLoS Comput Biol. 2016 Jul 25;12(7):e1005014.
PMID: 27454812 | PMCID: PMC4959759 | EndNote Citation

Lancaster MC, Sobie EA. Improved Prediction of Drug-Induced Torsades de Pointes Through Simulations of Dynamics and Machine Learning Algorithms. Clin Pharmacol Ther. 2016 Oct;100(4):371-9
PMID: 26950176 | EndNote Citation

Krogh-Madsen T, Sobie EA, Christini DJ. Improving cardiomyocyte model fidelity and utility via dynamic electrophysiology protocols and optimization algorithms. J Physiol. 2016 May 1;594(9):2525-36. doi: 10.1113/JP270618
PMID: 26661516 | PMCID:PMC4850194 | EndNote Citation

Devenyi RA, Sobie EA. There and back again: Iterating between population-based modeling and experiments reveals surprising regulation of calcium transients in rat cardiac myocytes. J Mol Cell Cardiol. 2016 Jul;96:38-48.
PMID: 26235057 | PMCID:PMC4733425 | EndNote Citation

Neves-Zaph SR, Song RS. Development of computational models of cAMP signaling. Methods Mol Biol. 2015;1294:203-17.
PMID: 25783888 | EndNote Citation

Gallo, JM, Birtwistle MR. Network pharmacodynamic models for customized cancer therapy. Wiley Interdiscip Rev Syst Biol Med. 2015 Jul;7(4):243-51.
PMID: 25914386 | EndNote Citation

Azeloglu EU, Iyengar R. Good practices for building dynamical models in systems biology. Sci Signal. 2015 Apr 7;8(371).
PMID: 25852187 | EndNote Citation

Iyengar, R. Can intracellular cAMP dynamics enable scalable computation? Front Cell Neurosci. 2015 Mar 27;9:112.
PMID: 25870541 | EndNote Citation

Poláková E, Illaste A, Niggli E, Sobie EA. Maximal acceleration of Ca2+ release refractoriness by β-adrenergic stimulation requires dual activation of kinases PKA and CaMKII in mouse ventricular myocytes. J Physiol. 2015 Mar 15;593(6):1495-507
PMID: 25772298 | EndNote Citation

Birtwistle MR. Analytical reduction of combinatorial complexity arising from multiple protein modification sites. J R Soc Interface. 2015 Feb 6;12(103).
PMID: 25519995 | EndNote Citation

Bouhaddou M, Birtwistle MR. Dimerization-based Control of Cooperativity. Mol Biosyst. 2014 Jun 3;10(7):1824-32.
PMID: 24736836 | EndNote Citation

Cummins MA, Dalal PJ, Bugana M, Severi S, Sobie EA. Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence PLoS Comput Biol. 2014 Mar 27;10(3):e1003543
Article | PMID: 24675446 | PMCID: PMC3967944 |EndNote Citation

Clark NR, Hu KS, Feldmann AS, Kou Y, Chen EY, Duan Q, Ma'ayan A. The Characteristic Direction: A Geometrical Approach to Identify Differentially Expressed Genes. BMC Bioinformatics 2014 Mar 21;15:79.
PMID: 24650281 | PMCID: PMC4000056 |EndNote Citation

Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R. Interconnected network motifs control podocyte morphology and kidney function. Sci Signal. 2014 Feb 4;7(311):ra12
PMID: 24497609 | EndNote Citation

Zhang XY, Birtwistle MR, Gallo JM. A general network pharmacodynamic model-based design pipeline for customized cancer therapy applied to the VEGFR pathway. CPT Pharmacometrics Syst Pharmacol. 2014 Jan 15;3:e92.
PMID: 24429593 | EndNote Citation

Iyengar R. Complex diseases require complex therapies. EMBO Rep. 2013 Dec;14(12):1039-42.
PMID: 24232184 | EndNote Citation

Lee P, Sobie EA, Peskin CS. Computer simulation of voltage sensitive calcium ion channels in a dendritic spine. J Theor Biol. 2013 Dec 7;338:87-93.
PMID: 23999286 | EndNote Citation

Isaacson SA, Larabell CA, Le Gros MA, McQueen DM, Peskin CS. The influence of spatial variation in chromatin density determined by x-ray tomograms on the time to find DNA binding sites. Bull Math Biol. 2013 Nov;75(11):2093-117.
PMID: 23955281 | EndNote Citation

Zhao S, Nishimura T, Chen Y, Azeloglu EU, Gottesman O, Giannarelli C, Zafar MU, Benard L, Badimon JJ, Hajjar RJ, Goldfarb J, Iyengar R. Systems pharmacology of adverse event mitigation by drug combinations. Sci Transl Med. 2013 Oct 9;5(206):206ra140
PMID: 24107779 | Supplementary Materials | EndNote Citation

Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR. ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion. Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15437-42
PMID: 23986500 | EndNote Citation

Rangamani P, Lipshtat A, Azeloglu EU, Calizo RC, Hu M, Ghassemi S, Hone J, Scarlata S, Neves SR, Iyengar R. Decoding Information in Cell Shape Cell. 2013 Sep 12154(6):1356-69
Article | PMID: 24034255 | EndNote Citation

Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford). 2013 Jun 21;2013:bat045.
PMID: 23794736 | PMCID: PMC3689438 | EndNote Citation

Tan CM, Chen EY, Dannenfelser R, Clark NR, Ma'ayan A. Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics. 2013 Aug 1;29(15):1872-8.
PMID: 23749960 | PMCID: PMC3712222 | EndNote Citation

Poláková E, Sobie EA. Alterations in T-tubule and dyad structure in heart disease: challenges and opportunities for computational analyses. Cardiovasc Res. 2013 May 1;98(2):233-9.
PMID: 23396602 | PMCID: PMC3633159 | EndNote Citation

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013 Apr 15;14:128.
Article | PMID: 23586463 | PMCID: PMC3637064 | EndNote Citation

Zhong Y, Chen EY, Liu R, Chuang PY, Mallipattu SK, Tan CM, Clark NR, Deng Y, Klotman PE, Ma'ayan A, He JC. Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase. J Am Soc Nephrol. 2013 Apr;24(5):801-11.
PMID: 23559582 | PMCID: PMC3636790 | EndNote Citation

Duan Q, Kou Y, Clark NR, Gordonov S, Ma'ayan A. Metasignatures Identify Two Major Subtypes of Breast Cancer. CPT Pharmacometrics Syst Pharmacol. 2013 Mar 27;2:e35.
Article | PMID: 23836026 | PMCID: PMC3615534 | EndNote Citation

Lee YS, Liu OZ, Hwang HS, Knollmann BC, Sobie EA. Parameter sensitivity analysis of stochastic models provides insights into cardiac calcium sparks. Biophys J. 2013 Mar 5;104(5):1142-50.
PMID: 23473497 | EndNote Citation

Jenkins SL, Ma'ayan A. Systems pharmacology meets predictive, preventive, personalized and participatory medicine Pharmacogenomics. 2013 Jan;14(2):119-22
PMID: 23327571 | PMCID: PMC3605723 | EndNote Citation

Hansen J, Iyengar R. Computation as the Mechanistic Bridge Between Precision Medicine and Systems Therapeutics Clin Pharmacol Ther. 2013 Jan;93(1):117-28.
PMID: 23212109 | EndNote Citation

Ma'ayan A. Colliding Dynamical Complex Network Models: Biological Attractors versus Attractors from Material Physics. Biophys J. 2012 Nov 7;103(9):1816-7
PMID: 23199907| PMCID: PMC3491669 | EndNote Citation

Gautier EL, Shay T, Miller J, Greter M, Jakubzick C, Ivanov S, Helft J, Chow A, Elpek KG, Gordonov S, Mazloom AR, Ma'ayan A, Chua WJ, Hansen TH, Turley SJ, Merad M, Randolph GJ; the Immunological Genome Consortium. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol. 2012 Sep 30. doi: 10.1038/ni.2419
PMID: 23023392 | PMCID: PMC3558276 | EndNote Citation

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A. Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol. 2012 Jul 23;6(1):89
PMID: 22824380 | PMCID: PMC344364 | EndNote Citation

Zhou Q, Lv H, Mazloom AR, Xu H, Ma'ayan A, Gallo JM Activation of Alternate Pro-Survival Pathways Accounts for Acquired Sunitinib Resistance in U87MG Glioma Xenografts. J Pharmacol Exp Ther. 2012 Aug 6
PMID: 22869928 | PMCID: PMC3477209 | Abstract

Dannenfelser R, Clark NR, Ma'ayan A. Genes2FANs: connecting genes through functional association networks. BMC Bioinformatics. 2012 Jul 2;13(1):156
PMID: 22748121 | PMCID: PMC3472228 | EndNote Citation

Sirovich L. The faithful copy neuron. J Comput Neurosci. 2012 Jun;32(3):377-85
PMID: 22234837 | EndNote Citation

Stinchcombe A, Peskin CS, Tranchina D. Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression. Physical Review. E, Statistical, nonlinear, and soft matter physics 85, 061919 (2012)
Abstract | EndNote Citation

Sarkar AX, Christini DJ, Sobie EA. Exploiting mathematical models to illuminate electrophysiological variability between individuals. J Physiol. 2012 Jun 1;590(Pt 11):2555-67.
PMID: 22495591 | PMCID: PMC3424714 | EndNote Citation

Kou Y, Betancur C, Xu H, Buxbaum JD, Ma'ayan A. Network-and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. Am J Med Genet C Semin Med Genet. 2012 May 15;160C(2):130-42.
PMID: 22499558 | PMCID: PMC3505691 | EndNote Citation

Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 Apr 4;485(7397):242-5
PMID: 22495311 | PMCID:PMC3613847 | EndNote Citation

Iyengar R, Zhao S, Chung SW, Mager DE, Gallo JM. Merging systems biology with pharmacodynamics. Sci Transl Med. 2012 Mar 21;4(126):126ps7.
PMID: 22440734 | EndNote Citation | Supplementary Materials

Jin Y, Ratnam K, Chuang PY, Fan Y, Zhong Y, Dai Y, Mazloom AR, Chen EY, D'Agati V, Xiong H, Ross MJ, Chen N, Ma'ayan A, He JC. A systems approach identifies HIPK2 as a key regulator of kidney fibrosis. Nat Med. 2012 Mar 11;18(4):580-8.
PMID: 22406746 | EndNote Citation | Article

Hwangpo TA, Jordan D, Premsrirut PK, Jayamaran G, Licht J, Iyengar R, Neves SR. GRIN modulates Sprouty repression of MAPK activation by growth factor stimulation. J Biol Chem. 2012 Mar 1.
PMID: 22383529 | EndNote Citation

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

Wenderski WC, Neves SR. Modeling of spatial intracellular signaling events in neurons. Methods Enzymol. 2012;505:105-24
PMID: 22289450

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

Ding J, Xu H, Faiola F, Ma'ayan A, Wang J Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res. 2012 Jan;22(1):155-67.
PMID: 22083510 | PMCID: PMC3252465 | 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 | PMCID: PMC3244772 | EndNote Citation

Liu OZ, Lederer WJ, Sobie EA. Does the Goldilocks Principle apply to calcium release restitution in heart cells? J Mol Cell Cardiol. 2012 Jan;52(1):3-6.
PMID: 22056316 | EndNote Citation

Hansen J, Zhao S, Iyengar R. Systems pharmacology of complex diseases. Ann N Y Acad Sci. 2011 Dec;1245:E1-5.
PMID: 22319785 | EndNote Citation

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 | PMCID: PMC3248428 | 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 | PMCID: PMC3238026 | 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 | PMCID: PMC3213042 | EndNote Citation

Sirovich L. Probabilistic reasoning in data analysis. Sci Signal. 2011 Sep 27;4(192):tr14.
PMID: 21954295 | PMCID: PMC3226815 | EndNote Citation

Hayot F. Simulations of stochastic biological phenomena. Sci Signal. 2011 Sep 27;4(192):tr13.
PMID: 21954294 | PMCID: PMC3225182 | 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 | PMCID: PMC3272496 | 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 | PMCID: PMC3196357 | 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 | PMCID: PMC3205944 | 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 | PMCID: PMC3193798 | EndNote Citation

Sobie EA, Lee YS, Jenkins SL, Iyengar R. Systems biology--biomedical modeling. Sci Signal. 2011 Sep 13;4(190):tr2
PMID: 21917716 | PMCID: PMC3188945 | 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 | PMCID: PMC3240740 | EndNote Citation

Sobie EA, Sarkar AX. Regression methods for parameter sensitivity analysis: applications to cardiac arrhythmia mechanisms. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:4657-60.
PMID: 22255376 | 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 | PMCID: PMCID: PMC3209525 | 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
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.
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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.
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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)
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.
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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.
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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