Publications

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. 7(1):e29239 (2012) PMID: 22235275

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 (2011) PMID: 22219718

Chen EY, Xu H, Gordonov S, Lim MP, Perkins MH, Ma’ayan A. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics 28(1):105-11 (2012) PMID: 22080467

He JC, Chuang PY, Ma'ayan A, Iyengar R. Systems biology of kidney diseases. Kidney Int. 81(1):22-39 (2012) PMID: 21881558

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

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

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. 6(10):e25535 (2011) PMID: 22043286

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

Ma'ayan A. Introduction to network analysis in systems biology. Sci Signal. 4(190):tr5 (2011) PMID: 21917719

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

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

Dannenfelser R, Lachmann A, Szenk M, Ma'ayan A. FNV: Light-weight Flash-based network and pathway viewer. Bioinformatics 27(8):1181-2 (2011) PMID: 21349871

Webb RL, Ma'ayan A. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code for Biol Med. 6:5 (2011) PMID: 21418653

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. 4(1):173 (2010) PMID: 21176149

Carcea I, Ma'ayan A, Mesias R, Sepulveda B, Salton SR, Benson DL. Flotillin-mediated endocytic events dictate cell type-specific responses to Semaphorin 3A. J Neuroscience 30(45):15317-29 (2010) PMID: 21068336

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 26(19):2438-44 (2010) PMID: 20709693

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 466(7308):829-34 (2010) PMID: 20703299

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. 107(34):15299-304 (2010) PMID: 20686112

Ma'ayan A, He JC. Protein kinase target discovery from genome-wide messenger RNA expression profiling. Mt Sinai J Med. 77(4):345-9 (2010) PMID: 20687179

MacArthur BD, Sanchez-Garcia RJ, Ma'ayan A. Microdynamics and criticality of adaptive regulatory networks. Phys Rev Lett. 104(16):168701 (2010) PMID: 20482087

Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Sci Signal. 3(118):ra30 (2010) PMID:20407125

Hernandez M, Lachmann A, Zhao S, Xiao K, Ma’ayan A. Inferring the sign of kinase-substrate interactions by combining SILAC phosphoproteomics with a literature-based mammalian kinome network. 10th IEEE International Conference on Bioinformatics and BioEngineering (2010) BIBE.

Xu H, Schaniel C, Lemischka IR, Ma’ayan A. Toward a complete in-silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip Rev Syst Biol Med. 2(6):708-33 (2010) PMID 20890967.

Lachmann A, Ma’ayan A. Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics 11, 87 (2010) PMID: 20152038

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 462, 358-362 (2009) PMID: 19924215

Macarthur BD, Lachmann A, Lemischka IR, Ma’ayan A. GATE: Software for the analysis and visualization of high-dimensional time-series expression data. Bioinformatics 26, 143-144 (2010) PMID: 19892805

Cordeddu V, Di Schiavi E, Pennacchio LA, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, et al. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet. 41, 1022 (2009) PMID: 19684605

Macarthur BD, Ma'ayan A, Lemischka IR. Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol. 10, 672 (2009) PMID: 19738627

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 9, 3303 (2009) PMID: 19562802

Macarthur BD, Ma'ayan A, Lemischka IR. Toward stem cell systems biology: from molecules to networks and landscapes. Cold Spring Harb Symp Quant Biol. 73, 211-5 (2008) PMID: 19329576

Lachmann A, Ma’ayan A. KEA: Kinase enrichment analysis. Bioinformatics 25, 684-6 (2009) PMID: 19176546

Ma'ayan A, Jenkins SL, Barash A, Iyengar R. Neuro2A differentiation by Galphai/o pathway. Sci Signal. 2(54):cm1 (2009) PMID: 19155528

Ma’ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn N, Posner JM, Flores T, Iyengar R. SNAVI: Desktop Application for Analysis and Visualization of Large-Scale Signaling Networks. BMC Syst Biol. 3, 10 (2009) PMID: 19154595

Ma’ayan A, Cecchi GA, Wagner J, Rao AR, Iyengar R, Stolovitzky G. Ordered Cyclic Motifs Contributes to Dynamic Stability in Biological and Engineered Networks. Proc Natl Acad Sci U S A. 105, 19235-40 (2008) PMID: 19033453

Ma’ayan A. Insights into the organization of biochemical regulatory networks using graph theory analyses. J Biol Chem. 284, 5451-5 (2009) PMID: 18940806

Ma’ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol. 2, 206-21 (2008) PMID: 19045817

Lu TC, Wang Z, Feng X, Chuang P, Fang W, Chen Y, Neves S, Ma’ayan A, Xiong H, Liu Y, Iyengar R, Klotman PE, He JC. Retinoic acid utilizes CREB and USF-1 in a transcriptional feed-forward loop in order to stimulate MKP1 expression in HIV-infected podocytes. Mol Cell Biol.28, 5785-94 (2008) PMID: 18625721

Bromberg KD, Ma’ayan A, Neves SR, Iyengar R. Design of a CB1 receptor signaling network to trigger neurite outgrowth. Science 320, 903-909 (2008) PMID: 18487186

Ma’ayan A, Lipshtat A, Iyengar R, Sontag ED. Proximity of Intracellular Regulatory Networks to Monotone Systems. IET Syst Biol. 2, 103-112 (2008) PMID: 18537452

Ma'ayan A. PubMedAlertMe - Standalone Windows-based PubMed SDI Software. Comput Biol Med. 38:620-622 (2008) PMID: 18402930

Lipshtat A, Purushothaman SP, Iyengar R, Ma'ayan A. Functions of bifans in context of multiple regulatory motifs in signaling network. Biophys J.  94, 2566-2579 (2008) PMID: 18178648

White AG, Ma'ayan A. Connecting seed lists of mammalian proteins using steiner trees. ACSSC 2007. Conference Record of the Forty-First Asilomar Conference on Signals, Systems and Computers, 2007. 4-7 Nov. 2007 page(s): 155-159 Pacific Grove, CA, USA

Caplan AJ, Ma'ayan A, Willis IM. Multiple kinases and system robustness: A link between Cdc37 and genome integrity. Cell Cycle 6:3145 (2007) PMID: 18075309

Posner JM, Berger SI, Ma’ayan A. Genes2Networks: connecting lists of proteins by using background literature-based mammalian networks. BMC Bioinformatics 8:372 (2007) PMID: 17916244

Berger SI, Iyengar R, Ma’ayan A. AVIS: AJAX Viewer of Interactive Signaling Networks. Bioinformatics 23, 2803-5 (2007) PMID: 17855420

Zaidel-Bar R, Itzkovitz S, Ma’ayan A, Iyengar R, Geiger B. Functional Atlas of the Integrin Adhesome. Nat Cell Biol. 9, 858 (2007) PMID: 17671451

Ma’ayan A, Jenkins SL, Goldfarb J, Iyengar R. Network analysis of FDA approved drugs and their targets. Mt Sinai J Med. 74, 27 (2007) PMID: 17516560

Hasseldine A, Lipshtat A, Iyengar R, Ma’ayan A. (2007) Modeling Cell Signaling Networks. In “Bioinformatics – From Genomes to Therapies" Vol. 2 Edited by Thomas Lengauer. Pages 829- 860 (WILEY-VCH, Weinheim, Germany)

Ma’ayan A, Gardiner K, Iyengar R. The cognitive phenotype of Down syndrome: Insights from intracellular network analysis, NeuroRx 3, 396 (2006) PMID: 16815222

Ma’ayan A, Lipshtat A, Iyengar R. Topology of resultant signaling network shaped by evolutionary pressure, Phys Rev E Stat Nonlin Soft Matter Phys. 73, 061912 (2006) PMID: 16906869

Ma’ayan A, Iyengar R. From components to regulatory network motifs in signaling networks. Brief Funct Genomic Proteomic. 5, 57 (2006) PMID: 16769680

Ma'ayan A, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells. Annu Rev Biophys Biomol Struct. 34, 319 (2005) PMID: 15869393

Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong NJ, Weng G, Ram PT, Rice JJ, Kershenbaum A, Stolovitzky GA, Blitzer RD, Iyengar R. Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 309 (5737), 1078 (2005) PMID: 16099987