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List of works by Avi Ma'ayan

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t4 workshop report: Pathways of Toxicity

scientific article (publication date: 2014)
Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

scientific article published on 19 February 2016
Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons

scientific article
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

scientific article
Lists2Networks: integrated analysis of gene/protein lists

scientific article
Flotillin-mediated endocytic events dictate cell type-specific responses to semaphorin 3A

scientific journal article
Krüppel-like factor 6 regulates mitochondrial function in the kidney

scientific article
Retinoic acid utilizes CREB and USF1 in a transcriptional feed-forward loop in order to stimulate MKP1 expression in human immunodeficiency virus-infected podocytes

scientific article published on 14 July 2008
Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers

scientific article published on 10 June 2016
Introduction to Network Analysis in Systems Biology

scientific article published on September 6, 2011
Systems approach to explore components and interactions in the presynapse

scientific article published on June 2009
Expression of HIV transgene aggravates kidney injury in diabetic mice

scientific article published on 16 January 2013
Interconnected network motifs control podocyte morphology and kidney function

scientific article
Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks

scholarly article
Network2Canvas: network visualization on a canvas with enrichment analysis

scientific article
Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase

scientific article published on 4 April 2013
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

scientific article published on 13 November 2017
Network integration and graph analysis in mammalian molecular systems biology

scientific article (publication date: September 2008)
Single-cell immune landscape of human atherosclerotic plaques

scientific article published on 07 October 2019
A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis

scientific article published on 9 October 2015
Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

scientific article published on 30 October 2017
Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis

scientific article
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud

scholarly article by Denis Torre et al published 28 November 2018 in Cell systems
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.

scientific article published on 15 February 2017
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions

scientific article published on 13 May 2015
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

scientific article
GATE: software for the analysis and visualization of high-dimensional time series expression data

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

scientific article published on 12 April 2012
Neuro2A differentiation by Galphai/o pathway

scientific article published on 20 January 2009
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

scientific article published on 10 October 2017
AVIS: AJAX viewer of interactive signaling networks

scientific article
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks

scientific article
Toward stem cell systems biology: from molecules to networks and landscapes

scientific article published on January 2008
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

scientific article
B-myb is an essential regulator of hematopoietic stem cell and myeloid progenitor cell development

scientific article published on 10 February 2014
ChEA3: transcription factor enrichment analysis by orthogonal omics integration

scientific article published on 01 July 2019
Genes2FANs: connecting genes through functional association networks

scientific article
ELK1 transcription factor linked to dysregulated striatal mu opioid receptor signaling network and OPRM1 polymorphism in human heroin abusers.

scientific article
Toward a complete in silico, multi-layered embryonic stem cell regulatory network

scientific article
L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures.

scientific article published on 6 February 2018
Systems pharmacology meets predictive, preventive, personalized and participatory medicine

scientific article published on January 2013
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells

scientific article
Proximity of intracellular regulatory networks to monotone systems

scientific article published on May 2008
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

scientific article
Introduction to statistical methods for analyzing large data sets: gene-set enrichment analysis

scientific article
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production

scientific article
Functions of bifans in context of multiple regulatory motifs in signaling networks

scientific article
Introduction to statistical methods to analyze large data sets: principal components analysis

scientific article
SIRT6 haploinsufficiency induces BRAF melanoma cell resistance to MAPK inhibitors via IGF signalling

scientific article published in Nature Communications
Metasignatures identify two major subtypes of breast cancer

scientific article published on 27 March 2013

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