Publications

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 14:128 (2013)

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. Journal of the American Society of Nephrology (2013) PMID: 23559582

Duan Q, Kou Y, Clark NR, Gordonov S, Ma'ayan A. Metasignatures Identify Two Major Subtypes of Breast Cancer. CPT: Pharmacometrics & Systems Pharmacology (2013)

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

Mallipattu SK, Liu R, Zhong Y, Chen EY, D'Agati V, Kaufman L, Ma'ayan A, Klotman PE, Chuang PY, He JC. Expression of HIV transgene aggravates kidney injury in diabetic mice. Kidney International (2013) PMID: 23325078

Ma'ayan A. Colliding dynamical complex network models: Biological attractors versus attractors from material physics. Biophysical Journal 103(9):1816-1817 (2012) PMID: 23199907

Rabinowitz KM, Wang Y, Chen E, Hovhannisyan Z, Chiang D, Berin MC, Dahan S, Chaussabel D, Ma'ayan A, Mayer L. Transforming Growth Factor-b Signaling Controls Activities of Human Intestinal CD8 T Suppressor Cells. Gastroenterology pii: S0016-5085(12)01744-1 (2012) PMID: 23232296

Clavel C, Grisanti L, Zemla R, Rezza A, Barros R, Sennett R, Mazloom AR, Chung CY, Cai X, Cai CL, Pevny L, Nicolis S, Ma'ayan A, Rendl M. Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors. Developmental Cell 23(5):981-94 (2012) PMID: 23153495

Macarthur BD, Sevilla A, Lenz M, Müller FJ, Schuldt BM, Schuppert AA, Ridden SJ, Stumpf PS, Fidalgo M, Ma'ayan A, Wang J, Lemischka IR. Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nature Cell Biology 14(11):1139-47 (2012) PMID: 23103910

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. Nature Immunology 13(11):1118-1128 (2012) PMID: 23023392

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A. Sets2Networks: network inference from repeated observations of sets. BMC Systems Biology 6(1):89 (2012) PMID 22824380

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. Journal of Pharmacology and Experimental Therapeutics 343(2):509-19 (2012) PMID: 22869928

Lee DF, Su J, Ang YS, Carvajal-Vergara X, Mulero-Navarro S, Pereira CF, Gingold J, Wang HL, Zhao R, Sevilla A, Darr H, Williamson AJ, Chang B, Niu X, Aguilo F, Flores ER, Sher YP, Hung MC, Whetton AD, Gelb BD, Moore KA, Snoeck HW, Ma'ayan A, Schaniel C, Lemischka IR. Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling. Cell Stem Cell 11(2):179-94 (2012) PMID: 22862944

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

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. American Journal of  Medical Genetics Part C: Seminars in Medical Genetics 160C(2):130-42 (2012) PMID: 22499558

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 485(7397):242-5 (2012) PMID: 22495311

Mallipattu SK, Liu R, Zheng F, Narla G, Ma'ayan A, Dikman S, Jain MK, Saleem M, D'Agati V, Klotman P, Chuang PY, He JC. Kruppel-Like factor 15 (KLF15) is a key regulator of podocyte differentiation. Journal of Biological Chemistry 287(23):19122-35 (2012) PMID: 22493483

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. Nature Medicine 18(4):580-8 (2012) PMID: 22406746

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 Computational Biology 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 International 81(1):22-39 (2012) PMID: 21881558

Xu H, Ma'ayan A. Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. Lecture Notes Computer Science 7058:15-22 (2011)

Ding J, Xu H, Faiola F, Ma'ayan A, Wang J. Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Research 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 for Biology and Medicine 6(1):15 (2011) PMID:  21995939

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

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

Clark NR, Ma'ayan A. Introduction to statistical methods to analyze large data sets: principal components analysis. Science Signaling 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 Biology and Medicine 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 Systems Biology 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. Journal of 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. Mount Sinai Journal of Medicine 77(4):345-9 (2010) PMID: 20687179

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

Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Science Signaling 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 Interdisciplinary Reviews: Systems Biology and Medicine 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. Nature Genetics. 41, 1022 (2009) PMID: 19684605

MacArthur BD, Ma'ayan A, Lemischka IR. Systems biology of stem cell fate and cellular reprogramming. Nature Reviews: Molecular Cell Biology 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 Harbor Symposium on Quantitative Biology 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. Science Signaling 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 Systems Biology 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. Journal of Biological Chemistry 284, 5451-5 (2009) PMID: 18940806

Ma’ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Systems Biology 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. Molecular and Cellular Biology 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 Systems Biology 2, 103-112 (2008) PMID: 18537452

Ma'ayan A. PubMedAlertMe - Standalone Windows-based PubMed SDI Software. Computers in Biology and Medicine 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. Biophysical Journal 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

Berger SI, Posner JM, 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. Nature Cell Biology 9, 858 (2007) PMID: 17671451

Ma’ayan A, Jenkins SL, Goldfarb J, Iyengar R. Network analysis of FDA approved drugs and their targets. Mount Sinai Journal of Medicine 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, Physical Review: E, Statistical, Nonlinear and Soft Matter Physics 73, 061912 (2006) PMID: 16906869

Ma’ayan A, Iyengar R. From components to regulatory network motifs in signaling networks. Briefings in Functional Genomics and Proteomics 5, 57 (2006) PMID: 16769680

Ma'ayan A, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells. Annual Review of Biophysics and Biomolecular Structure 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