All Stories

  1. An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

    Article • F1000Research, July 2016, Faculty of 1000, Ltd.

    Zichen Wang, Dr. Avi Ma'ayan

  2. Drug-induced adverse events prediction with the LINCS L1000 data

    Article • Bioinformatics, April 2016, Oxford University Press (OUP)

    Dr. Avi Ma'ayan

  3. Abstract B1-25: Data integration for illuminating the druggable genome

    Article • Cancer Research, November 2015, American Association for Cancer Research (AACR)

    Dr. Avi Ma'ayan

  4. Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool

    Article • November 2015, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Avi Ma'ayan

  5. A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis

    Article • PLoS Genetics, October 2015, PLOS

    Dr. Avi Ma'ayan

  6. An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin

    Article • Developmental Cell, September 2015, Elsevier

    Zichen Wang, Dr. Avi Ma'ayan

  7. Abstract SY10-04: Histone tail alterations in cellular senescence

    Article • Cancer Research, August 2015, American Association for Cancer Research (AACR)

    Dr. Avi Ma'ayan

  8. Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis

    Article • Molecular & Cellular Proteomics, July 2015, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr. Avi Ma'ayan

  9. Dynamics of the discovery process of protein-protein interactions from low content studies

    Article • BMC Systems Biology, June 2015, Springer Science + Business Media

    Zichen Wang, Dr. Avi Ma'ayan

  10. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions: Fig. 1.

    Article • Bioinformatics, May 2015, Oxford University Press (OUP)

    Dr. Avi Ma'ayan

  11. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme

    Article • Nature Communications, November 2014, Nature

    Zichen Wang, Dr. Avi Ma'ayan

  12. A blueprint of cell identity

    Article • Nature Biotechnology, October 2014, Nature

    Dr. Avi Ma'ayan

  13. Lean Big Data integration in systems biology and systems pharmacology

    Article • Trends in Pharmacological Sciences, September 2014, Elsevier

    Zichen Wang, Dr. Avi Ma'ayan

  14. Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

    Article • PLoS Computational Biology, August 2014, PLOS

    Dr. Avi Ma'ayan

  15. The characteristic direction: a geometrical approach to identify differentially expressed genes

    Article • BMC Bioinformatics, January 2014, Springer Science + Business Media

    Dr. Avi Ma'ayan

  16. ELK1 Transcription Factor Linked to Dysregulated Striatal Mu Opioid Receptor Signaling Network and OPRM1 Polymorphism in Human Heroin Abusers

    Article • Biological Psychiatry, October 2013, Elsevier

    Dr. Avi Ma'ayan

  17. Induction of a Hemogenic Program in Mouse Fibroblasts

    Article • Cell Stem Cell, August 2013, Elsevier

    Dr. Avi Ma'ayan

  18. Expression of HIV transgene aggravates kidney injury in diabetic mice

    Article • Kidney International, April 2013, Elsevier

    Dr. Avi Ma'ayan

  19. Transforming Growth Factor β Signaling Controls Activities of Human Intestinal CD8+T Suppressor Cells

    Article • Gastroenterology, March 2013, Elsevier

    Dr. Avi Ma'ayan

  20. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Zichen Wang, Dr. Avi Ma'ayan

  21. Systems pharmacology meets predictive, preventive, personalized and participatory medicine

    Article • Pharmacogenomics, January 2013, Future Medicine

    Dr. Avi Ma'ayan

  22. Quantitative Approaches to Model Pluripotency and Differentiation in Stem Cells

    Article • January 2013, Springer Science + Business Media

    Dr. Avi Ma'ayan

  23. Biological and Quantitative Models for Stem Cell Self-Renewal and Differentiation

    Article • January 2013, Elsevier

    Dr. Avi Ma'ayan

  24. ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome

    Article • January 2013, Springer Science + Business Media

    Dr. Avi Ma'ayan

  25. Colliding Dynamical Complex Network Models: Biological Attractors versus Attractors from Material Physics

    Article • Biophysical Journal, November 2012, Elsevier

    Dr. Avi Ma'ayan

  26. Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors

    Article • Developmental Cell, November 2012, Elsevier

    Dr. Avi Ma'ayan

  27. Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity

    Article • Nature, October 2012, Nature

    Dr. Avi Ma'ayan

  28. Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer

    Article • October 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Avi Ma'ayan

  29. Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability

    Article • American Journal of Medical Genetics Part C Seminars in Medical Genetics, April 2012, Wiley

    Dr. Avi Ma'ayan

  30. A systems approach identifies HIPK2 as a key regulator of kidney fibrosis

    Article • Nature Reports Stem Cells, March 2012, Nature

    Dr. Avi Ma'ayan

  31. Receptor Heteromerization Expands the Repertoire of Cannabinoid Signaling in Rodent Neurons

    Article • PLoS ONE, January 2012, PLOS

    Dr. Avi Ma'ayan

  32. New Frontiers of Network Analysis in Systems Biology

    Article • January 2012, Springer Science + Business Media

    Dr. Avi Ma'ayan

  33. Network Pharmacology to Aid the Drug Discovery Process

    Article • January 2012, Springer Science + Business Media

    Dr. Avi Ma'ayan

  34. Systems biology of kidney diseases

    Article • Kidney International, January 2012, Elsevier

    Dr. Avi Ma'ayan

  35. Sets2Networks: network inference from repeated observations of sets

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Dr. Avi Ma'ayan

  36. Genes2FANs: connecting genes through functional association networks

    Article • BMC Bioinformatics, January 2012, Springer Science + Business Media

    Dr. Avi Ma'ayan

  37. Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes

    Article • PLoS Computational Biology, December 2011, PLOS

    Dr. Avi Ma'ayan

  38. Oct4 links multiple epigenetic pathways to the pluripotency network

    Article • Cell Research, November 2011, Nature

    Dr. Avi Ma'ayan

  39. Chronic Morphine Alters the Presynaptic Protein Profile: Identification of Novel Molecular Targets Using Proteomics and Network Analysis

    Article • PLoS ONE, October 2011, PLOS

    Dr. Avi Ma'ayan

  40. Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

    Article • Source Code for Biology and Medicine, January 2011, Springer Science + Business Media

    Dr. Avi Ma'ayan

  41. Mesenchymal and haematopoietic stem cells form a unique bone marrow niche

    Article • Nature, August 2010, Nature

    Dr. Avi Ma'ayan

  42. Protein Kinase Target Discovery From Genome-Wide Messenger RNA Expression Profiling

    Article • Mount Sinai Journal of Medicine A Journal of Translational and Personalized Medicine, July 2010, Wiley

    Dr. Avi Ma'ayan

  43. Microdynamics and Criticality of Adaptive Regulatory Networks

    Article • Physical Review Letters, April 2010, American Physical Society (APS)

    Dr. Avi Ma'ayan

  44. Toward a complete in silico , multi-layered embryonic stem cell regulatory network

    Article • WIREs Systems Biology and Medicine, March 2010, Wiley

    Dr. Avi Ma'ayan

  45. Lists2Networks: Integrated analysis of gene/protein lists

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Dr. Avi Ma'ayan

  46. Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network

    Article • January 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Avi Ma'ayan

  47. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells

    Article • BMC Systems Biology, January 2010, Springer Science + Business Media

    Dr. Avi Ma'ayan

  48. Systems-level dynamic analyses of fate change in murine embryonic stem cells

    Article • Nature, November 2009, Nature

    Dr. Avi Ma'ayan, Edoardo Airoldi

  49. Systems biology of stem cell fate and cellular reprogramming

    Article • Nature Reviews Molecular Cell Biology, September 2009, Nature

    Dr. Avi Ma'ayan

  50. Systems approach to explore components and interactions in the presynapse

    Article • PROTEOMICS, June 2009, Wiley

    Dr. Avi Ma'ayan

  51. PubMedAlertMe—Standalone Windows-based PubMed SDI software application

    Article • Computers in Biology and Medicine, May 2008, Elsevier

    Dr. Avi Ma'ayan

  52. Functions of Bifans in Context of Multiple Regulatory Motifs in Signaling Networks

    Article • Biophysical Journal, April 2008, Elsevier

    Dr. Avi Ma'ayan

  53. Multiple Kinases and System Robustness: A Link Between Cdc37 and Genome Integrity

    Article • Cell Cycle, December 2007, Taylor & Francis

    Dr. Avi Ma'ayan

  54. Connecting Seed Lists of Mammalian Proteins Using Steiner Trees

    Article • November 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Avi Ma'ayan

  55. Functional atlas of the integrin adhesome

    Article • Nature, August 2007, Nature

    Dr. Avi Ma'ayan

  56. Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

    Article • Nature Reports Climate Change, June 2007, Nature

    Dr. Avi Ma'ayan

  57. Network analysis of FDA approved drugs and their targets

    Article • Mount Sinai Journal of Medicine A Journal of Translational and Personalized Medicine, January 2007, Wiley

    Dr. Avi Ma'ayan

  58. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

    Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Dr. Avi Ma'ayan

  59. The cognitive phenotype of Down syndrome: Insights from intracellular network analysis

    Article • NeuroRx, July 2006, Springer Science + Business Media

    Dr. Avi Ma'ayan

  60. The cognitive phenotype of Down syndrome: Insights from intracellular network analysis

    Article • Neurotherapeutics, July 2006, Springer Science + Business Media

    Dr. Avi Ma'ayan

  61. Topology of resultant networks shaped by evolutionary pressure

    Article • Physical Review E, June 2006, American Physical Society (APS)

    Dr. Avi Ma'ayan

  62. Toward Predictive Models of Mammalian Cells

    Article • Annual Review of Biophysics and Biomolecular Structure, June 2005, Annual Reviews

    Dr. Avi Ma'ayan