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Avi Ma'ayan

TitleASSOCIATE PROFESSOR
InstitutionMount Sinai
DepartmentPharmacology and Systems Therapeutics
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     Bibliographic 
     selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Poultney CS, Goldberg AP, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnström K, Palotie A, Daly MJ, Ma'ayan A, Fromer M, Buxbaum JD. Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet. 2013 Oct 3; 93(4):607-19.
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    2. Jakubzick C, Gautier EL, Gibbings SL, Sojka DK, Schlitzer A, Johnson TE, Ivanov S, Duan Q, Bala S, Condon T, van Rooijen N, Grainger JR, Belkaid Y, Ma'ayan A, Riches DW, Yokoyama WM, Ginhoux F, Henson PM, Randolph GJ. Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity. 2013 Sep 19; 39(3):599-610.
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    3. 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; 2013:bat045.
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    4. Pereira CF, Chang B, Qiu J, Niu X, Papatsenko D, Hendry CE, Clark NR, Nomura-Kitabayashi A, Kovacic JC, Ma'ayan A, Schaniel C, Lemischka IR, Moore K. Induction of a hemogenic program in mouse fibroblasts. Cell Stem Cell. 2013 Aug 1; 13(2):205-18.
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    5. 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.
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    6. Sillivan SE, Whittard JD, Jacobs MM, Ren Y, Mazloom AR, Caputi FF, Horvath M, Keller E, Ma'ayan A, Pan YX, Chiang LW, Hurd YL. ELK1 transcription factor linked to dysregulated striatal mu opioid receptor signaling network and OPRM1 polymorphism in human heroin abusers. Biol Psychiatry. 2013 Oct 1; 74(7):511-9.
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    7. 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; 14:128.
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    8. 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.
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    9. Duan Q, Kou Y, Clark NR, Gordonov S, Ma'ayan A. Metasignatures identify two major subtypes of breast cancer. CPT Pharmacometrics Syst Pharmacol. 2013; 2:e35.
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    10. 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 Int. 2013 Apr; 83(4):626-34.
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    11. Jenkins SL, Ma'ayan A. Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics. 2013 Jan; 14(2):119-22.
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    12. Rabinowitz KM, Wang Y, Chen EY, Hovhannisyan Z, Chiang D, Berin MC, Dahan S, Chaussabel D, Ma'ayan A, Mayer L. Transforming growth factor ß signaling controls activities of human intestinal CD8(+)T suppressor cells. Gastroenterology. 2013 Mar; 144(3):601-612.e1.
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    13. 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. Dev Cell. 2012 Nov 13; 23(5):981-94.
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    14. Ma'ayan A. Colliding dynamical complex network models: biological attractors versus attractors from material physics. Biophys J. 2012 Nov 7; 103(9):1816-7.
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    15. 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. Nat Cell Biol. 2012 Nov; 14(11):1139-47.
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    16. 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. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat Immunol. 2012 Nov; 13(11):1118-28.
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    17. Zhou Q, Lv H, Mazloom AR, Xu H, Ma'ayan A, Gallo JM. Activation of alternate prosurvival pathways accounts for acquired sunitinib resistance in U87MG glioma xenografts. J Pharmacol Exp Ther. 2012 Nov; 343(2):509-19.
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    18. 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. 2012 Aug 3; 11(2):179-94.
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    19. Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma'ayan A. Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol. 2012; 6:89.
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    20. Dannenfelser R, Clark NR, Ma'ayan A. Genes2FANs: connecting genes through functional association networks. BMC Bioinformatics. 2012; 13:156.
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    21. 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.
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    22. 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. J Biol Chem. 2012 Jun 1; 287(23):19122-35.
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    23. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 May 10; 485(7397):242-5.
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    24. 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 Apr; 18(4):580-8.
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    25. 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.
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    26. Mazloom AR, Dannenfelser R, Clark NR, Grigoryan AV, Linder KM, Cardozo TJ, Bond JC, Boran AD, 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. 2011 Dec; 7(12):e1002319.
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    27. 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.
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    28. 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.
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    29. Abul-Husn NS, Annangudi SP, Ma'ayan A, Ramos-Ortolaza DL, Stockton SD, 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.
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    30. 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. 2011; 6:15.
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    31. Ma'ayan A. Introduction to network analysis in systems biology. Sci Signal. 2011 Sep 13; 4(190):tr5.
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    32. 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.
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    33. 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.
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    34. He JC, Chuang PY, Ma'ayan A, Iyengar R. Systems biology of kidney diseases. Kidney Int. 2012 Jan; 81(1):22-39.
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    35. Webb RL, Ma'ayan A. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol Med. 2011; 6:5.
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    36. 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.
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    37. 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; 4:173.
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    38. 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 Neurosci. 2010 Nov 10; 30(45):15317-29.
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    39. 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. 2010 Nov-Dec; 2(6):708-33.
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    40. 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.
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    41. 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.
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    42. 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.
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    43. 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.
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    44. Berger SI, Ma'ayan A, Iyengar R. Systems pharmacology of arrhythmias. Sci Signal. 2010; 3(118):ra30.
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    45. MacArthur BD, Sánchez-García RJ, Ma'ayan A. Microdynamics and criticality of adaptive regulatory networks. Phys Rev Lett. 2010 Apr 23; 104(16):168701.
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    46. Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics. 2010; 11:87.
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    47. 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.
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    48. 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.
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    49. 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.
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    50. 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.
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    51. 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):3303-15.
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    52. 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.
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    53. Lachmann A, Ma'ayan A. KEA: kinase enrichment analysis. Bioinformatics. 2009 Mar 1; 25(5):684-6.
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    54. Ma'ayan A, Jenkins SL, Barash A, Iyengar R. Neuro2A differentiation by Galphai/o pathway. Sci Signal. 2009; 2(54):cm1.
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    55. 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; 3:10.
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    56. 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.
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    57. 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.
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    58. Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. IET Syst Biol. 2008 Sep; 2(5):206-21.
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    59. Bromberg KD, Ma'ayan A, Neves SR, Iyengar R. Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science. 2008 May 16; 320(5878):903-9.
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    60. 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.
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    61. Ma'ayan A. PubMedAlertMe--standalone Windows-based PubMed SDI software application. Comput Biol Med. 2008 May; 38(5):620-2.
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    62. Lipshtat A, Purushothaman SP, Iyengar R, Ma'ayan A. Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophys J. 2008 Apr 1; 94(7):2566-79.
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    63. Berger SI, Posner JM, Ma'ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics. 2007; 8:372.
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    64. Caplan AJ, Ma'ayan A, Willis IM. Multiple kinases and system robustness: a link between Cdc37 and genome integrity. Cell Cycle. 2007 Dec 15; 6(24):3145-7.
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    65. Berger SI, Iyengar R, Ma'ayan A. AVIS: AJAX viewer of interactive signaling networks. Bioinformatics. 2007 Oct 15; 23(20):2803-5.
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    66. Zaidel-Bar R, Itzkovitz S, Ma'ayan A, Iyengar R, Geiger B. Functional atlas of the integrin adhesome. Nat Cell Biol. 2007 Aug; 9(8):858-67.
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    67. Ma'ayan A, Jenkins SL, Goldfarb J, Iyengar R. Network analysis of FDA approved drugs and their targets. Mt Sinai J Med. 2007 Apr; 74(1):27-32.
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    68. Ma'ayan A, Gardiner K, Iyengar R. The cognitive phenotype of Down syndrome: insights from intracellular network analysis. NeuroRx. 2006 Jul; 3(3):396-406.
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    69. Ma'ayan A, Lipshtat A, Iyengar R. Topology of resultant networks shaped by evolutionary pressure. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun; 73(6 Pt 1):061912.
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    70. Ma'ayan A, Iyengar R. From components to regulatory motifs in signalling networks. Brief Funct Genomic Proteomic. 2006 Mar; 5(1):57-61.
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    71. 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. 2005 Aug 12; 309(5737):1078-83.
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    72. Ma'ayan A, Blitzer RD, Iyengar R. Toward predictive models of mammalian cells. Annu Rev Biophys Biomol Struct. 2005; 34:319-49.
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    73. Axer-Siegel R, Snir M, Ma'ayan A, Na'or N, Davidson S, Weinberger D, Yassur Y. Retinopathy of prematurity and surfactant treatment. J Pediatr Ophthalmol Strabismus. 1996 May-Jun; 33(3):171-4.
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    Mount Sinai Profiles is managed by Conduits - The Institutes for Translational Sciences at Icahn School of Medicine, supported by the National Center for Research Resources and the National Center for Advancing Translational Sciences of the National Institutes of Health through Grant Number UL1TR000067