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List of works by Avi Ma'ayan

A blueprint of cell identity

scientific article published on October 2014

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

scientific article published on 11 March 2012

AVIS: AJAX viewer of interactive signaling networks

scientific article

Activation of alternate prosurvival pathways accounts for acquired sunitinib resistance in U87MG glioma xenografts

scientific article

Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth.

scientific article

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

scientific article published on 5 August 2015

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

BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud

scholarly article published 20 June 2018

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

scientific article published on 01 July 2019

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

scientific article

Chronic morphine alters the presynaptic protein profile: identification of novel molecular targets using proteomics and network analysis

scientific article

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

scientific article published on 10 October 2017

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

scientific article published on November 7, 2012

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

scientific article published on 30 October 2017

Complex systems biology

scientific article

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees

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

article

Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells

scientific article

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics

scientific article

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

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

scientific article published on 27 February 2018

Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent

scientific article published on 27 December 2018

Dermal sheath contraction powers stem cell niche relocation during hair cycle regression

scientific article published on 19 December 2019

Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth

scientific article

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

scientific article

Differential cytokine contributions of perivascular haematopoietic stem cell niches

scientific article published on 20 February 2017

Direct activation of PP2A for the treatment of tyrosine kinase inhibitor-resistant lung adenocarcinoma

scientific article published on 21 February 2019

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures

article

Drug-induced adverse events prediction with the LINCS L1000 data

scientific article

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets

scientific article

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules

scientific article published on 19 February 2022

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

scientific article

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

scientific article

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

scientific article

Elysium: RNA-seq Alignment in the Cloud

scholarly article published 2 August 2018

Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications

Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells

scientific article published on 15 April 2019

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

scientific article

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

scientific article

Expression of HIV transgene aggravates kidney injury in diabetic mice

scientific article published on 16 January 2013

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

scientific article published on 10 November 2011

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.

scientific article published on 26 September 2016

FNV: light-weight flash-based network and pathway viewer

scientific article

Far away from the lamppost

scientific article published on 11 December 2018

Fetal liver hematopoietic stem cell niches associate with portal vessels

scientific article

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

scientific journal article

Formation of regulatory patterns during signal propagation in a Mammalian cellular network

scientific article

From components to regulatory motifs in signalling networks

scientific article published on 20 February 2006

Functional atlas of the integrin adhesome

scientific article (publication date: August 2007)

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

scientific article

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

scientific article

GEN3VA: aggregation and analysis of gene expression signatures from related studies

scientific article (publication date: 15 November 2016)

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

Gene set predictor for post-treatment Lyme disease

scientific article published in 2022

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

scientific article (publication date: November 2012)

Genes2FANs: connecting genes through functional association networks

scientific article

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

scientific article published on 4 October 2007

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

scientific article

Geneshot: search engine for ranking genes from arbitrary text queries

scientific article published on 01 July 2019

Global phosphorylation analysis of beta-arrestin-mediated signaling downstream of a seven transmembrane receptor (7TMR).

scientific article

Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production ⬇️

scientific article

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

scientific article

Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder

scientific article

Induction of a hemogenic program in mouse fibroblasts

scientific article published on 13 June 2013

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

article published in 2010

Insights into the organization of biochemical regulatory networks using graph theory analyses

scientific article published on 20 October 2008

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.

scientific article published on 2 January 2018

Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks

scientific article published on 22 May 2018

Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens

scientific article published on 23 December 2016

Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma

scientific article

Interconnected network motifs control podocyte morphology and kidney function

scientific article

Introduction to Network Analysis in Systems Biology ⬇️

scientific article published on September 6, 2011

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

scientific article

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

scientific article

KEA: kinase enrichment analysis

scientific article published on 28 January 2009

Kruppel-like factor 15 (KLF15) is a key regulator of podocyte differentiation

scientific journal article

Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers

scientific article published on 10 June 2016

Krüppel-like factor 6 regulates mitochondrial function in the kidney

scientific article

Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans

scientific article published on 01 June 2021

L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures.

scientific article published on 6 February 2018

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

scientific article

Lean Big Data integration in systems biology and systems pharmacology

scientific article

Lists2Networks: integrated analysis of gene/protein lists

scientific article

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

scholarly article published 14 September 2017

Massive mining of publicly available RNA-seq data from human and mouse

scientific article published on 10 April 2018

Metasignatures identify two major subtypes of breast cancer

scientific article published on 27 March 2013

Microdynamics and criticality of adaptive regulatory networks.

scientific article published on 19 April 2010

Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes

scientific article published on 05 September 2013

Mining data and metadata from the gene expression omnibus

article

Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis

scientific article published on 6 July 2015

Multiple kinases and system robustness: a link between Cdc37 and genome integrity

scientific article

Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair

scientific article

Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity

scientific article published on 28 October 2012

Network analysis of FDA approved drugs and their targets

scientific article

Network integration and graph analysis in mammalian molecular systems biology

scientific article (publication date: September 2008)

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

scientific article published on 12 April 2012

Network2Canvas: network visualization on a canvas with enrichment analysis

scientific article

Neuro2A differentiation by Galphai/o pathway

scientific article published on 20 January 2009

Oct4 links multiple epigenetic pathways to the pluripotency network

scientific article published on 15 November 2011

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

scholarly article

Pharos: Collating protein information to shed light on the druggable genome

scientific article

Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration

scientific article published on 15 August 2016

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.

scientific article published on 4 November 2017

Predicting opioid dependence from electronic health records with machine learning

scientific article published on 29 January 2019

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

scientific article published in November 2015

Prioritizing Pain-Associated Targets with Machine Learning

scientific article published on 20 February 2021

Protein kinase target discovery from genome-wide messenger RNA expression profiling

scientific article published on July 2010

Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte

scientific article

Proximity of intracellular regulatory networks to monotone systems

scientific article published on May 2008

PubMedAlertMe--standalone Windows-based PubMed SDI software application

scientific article published on 9 April 2008

Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction

scientific article

Receptor heteromerization expands the repertoire of cannabinoid signaling in rodent neurons

scientific article

Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes

scientific article

Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling

scientific article

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

scientific article published on 4 April 2013

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".

scientific article

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

scientific article published in Nature Communications

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

scientific article

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

scientific article

Sets2Networks: network inference from repeated observations of sets

scientific article

Short-term LXR activation improves epidermal barrier features in mild-to-moderate atopic dermatitis: a randomized controlled trial

scientific article published on 19 March 2018

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

scientific article

SigCom LINCS: data and metadata search engine for a million gene expression signatures

scientific article published in 2022

Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.

scientific article

Single-cell immune landscape of human atherosclerotic plaques

scientific article published on 07 October 2019

Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors

scientific article published on November 2012

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.

scientific article published on 19 June 2018

Synaptic, transcriptional and chromatin genes disrupted in autism

scientific article

Systems approach to explore components and interactions in the presynapse

scientific article published on June 2009

Systems biology of kidney diseases

scientific article published on 31 August 2011

Systems biology of stem cell fate and cellular reprogramming

scientific article published on 09 September 2009

Systems pharmacology meets predictive, preventive, personalized and participatory medicine

scientific article published on January 2013

Systems pharmacology of arrhythmias

scientific article

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

scientific article

Temporal proteomic profiling of postnatal human cortical development

article

Temporal proteomic profiling of postnatal human cortical development

scientific article published on 05 December 2018

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

scientific article published on 24 November 2017

The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways

scientific article published on 31 October 2019

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

scientific article

The cognitive phenotype of Down syndrome: insights from intracellular network analysis

scientific article published on July 2006

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

scientific article published on 03 July 2016

Topology of resultant networks shaped by evolutionary pressure

scientific article

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

scientific article

Toward predictive models of mammalian cells

scientific article

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

scientific article published on January 2008

Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis.

scientific article published in November 2017

Transforming growth factor β signaling controls activities of human intestinal CD8(+)T suppressor cells

scientific article published on 08 December 2012

Unexplored therapeutic opportunities in the human genome.

scientific article published on 23 February 2018

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.

scientific article published in July 2018

modEnrichr: a suite of gene set enrichment analysis tools for model organisms

scientific article published on 01 July 2019

t4 workshop report: Pathways of Toxicity

scientific article (publication date: 2014)

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