Avi Ma’ayan

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.

How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (4)

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.⚑
  2025 L1 76/100 ⚑
• RummaGEO: Automatic mining of human and mouse gene sets from GEO.
  2024 L1 63/100
• D2H2: diabetes data and hypothesis hub.
  2023
• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
  2016 L1 74/100

4 assessed by us (1 reproduced) · 360 not yet assessed — every PubMed paper on record, linked below.

• NIH Sample 2[183]

  Open MIND · 2034
  not yet assessed
• NIH Sample 2

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[181]

  Open MIND · 2034
  not yet assessed
• Project-1

  Open MIND · 2034
  not yet assessed
• Project-1

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[191]

  Open MIND · 2034
  not yet assessed
• Hexyl Nayori[1]

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[190]

  Open MIND · 2034
  not yet assessed
• Hexyl Nayori

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[184]

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[185]

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[192]

  Open MIND · 2034
  not yet assessed
• NIH Sample 2[182]

  Open MIND · 2034
  not yet assessed
• The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs ↗

  Journal of Molecular Biology · 2026 · PMID 41506317
  not yet assessed
• Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets ↗

  Nature Cancer · 2026 · PMID 42286338
  not yet assessed
• A tool based on objective data to identify patients at elevated risk of hospital-onset <i>Staphylococcus aureus</i> bacteremia: a nested case–control study ↗

  Antimicrobial Stewardship & Healthcare Epidemiology · 2026 · PMID 42038617
  not yet assessed
• Cerebellar microRNA-206 tunes Purkinje neuron firing dynamics to control sensorimotor gating ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026 · PMID 42427608
  not yet assessed
• GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets ↗

  Patterns · 2026
  not yet assessed
• ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow ↗

  Nucleic Acids Research · 2026 · PMID 42163770
  not yet assessed
• L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine ↗

  Nucleic Acids Research · 2025 · PMID 40308216
  not yet assessed
• Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures ↗

  Cancer Cell · 2025 · PMID 40749670
  not yet assessed
• Playbook workflow builder: Interactive construction of bioinformatics workflows ↗

  PLoS Computational Biology · 2025 · PMID 40179105
  not yet assessed
• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets⚑

  GigaScience · 2025 · PMID 40208796
  L1 76/100 ⚑
• Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases ↗

  Current Protocols · 2025 · PMID 40956607
  not yet assessed
• lncRNAlyzr: Enrichment Analysis for lncRNA Sets ↗

  Journal of Molecular Biology · 2025 · PMID 40133794
  not yet assessed
• Molecular signatures and signaling interactions of the hair follicle stem cell niche ↗

  Journal of Investigative Dermatology · 2025 · PMID 41407191
  not yet assessed
• The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40832351
  not yet assessed
• The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• ChEA-KG: Human Transcription Factor Regulatory Network with a Knowledge Graph Interactive User Interface ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40832173
  not yet assessed
• Abstract 5019: Genomic landscape, tumor heterogeneity and immune-related post-translational regulation in cutaneous melanoma ↗

  Cancer Research · 2025
  not yet assessed
• Abstract 6290: sc2DAT: workflow for targeting tumor subpopulations of single cells ↗

  Cancer Research · 2025
  not yet assessed
• Abstract 6305: hGRN-ChEAR: human transcription factor regulatory network with a knowledge graph interactive user interface ↗

  Cancer Research · 2025
  not yet assessed
• Abstract 1079: L2S2: Chemical perturbation and CRISPR KO LINCS L1000 signature search engine ↗

  Cancer Research · 2025
  not yet assessed
• A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40501705
  not yet assessed
• NIH Sample 2[184] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[185] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[190] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[183] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[191] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[192] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[182] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2[181] ↗

  nmrXiv · 2025
  not yet assessed
• NIH Sample 2 ↗

  nmrXiv · 2025
  not yet assessed
• Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources ↗

  Nucleic Acids Research · 2024 · PMID 39565209
  not yet assessed
• Pan-cancer proteogenomics characterization of tumor immunity ↗

  Cell · 2024 · PMID 38359819
  not yet assessed
• Comprehensive proteogenomic characterization of rare kidney tumors ↗

  Cell Reports Medicine · 2024 · PMID 38703764
  not yet assessed
• Programming a Ferroptosis‐to‐Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy ↗

  Advanced Science · 2024 · PMID 38441406
  not yet assessed
• Rummagene: massive mining of gene sets from supporting materials of biomedical research publications ↗

  Communications Biology · 2024 · PMID 38643247
  not yet assessed
• RummaGEO: Automatic mining of human and mouse gene sets from GEO

  Patterns · 2024 · PMID 39569206
  L1 63/100
• Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis ↗

  Intensive Care Medicine · 2024 · PMID 39432104
  not yet assessed
• Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics ↗

  Cell Reports Methods · 2024 · PMID 39127042
  not yet assessed
• Regulatory elements in SEM1-DLX5-DLX6 (7q21.3) locus contribute to genetic control of coronal nonsyndromic craniosynostosis and bone density-related traits ↗

  Genetics in Medicine Open · 2024 · PMID 39345948
  not yet assessed
• Programming a Ferroptosis‐to‐Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy (Adv. Sci. 17/2024) ↗

  Advanced Science · 2024
  not yet assessed
• RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 38645198
  not yet assessed
• Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows from a Network of Microservices ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes Towards a Purkinje Fiber Fate ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 39386729
  not yet assessed
• Abstract 3955: A proteogenomic study of high-grade glioma among adolescents and young adults ↗

  Cancer Research · 2024
  not yet assessed
• Abstract 7346: Optimizing pan-cancer driver pathway analysis from patient transcriptomics and phosphoproteomics ↗

  Cancer Research · 2024
  not yet assessed
• Abstract 4897: Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of tumors ↗

  Cancer Research · 2024
  not yet assessed
• Rummagene gene sets with descriptions 01172024 ↗

  Figshare · 2024
  not yet assessed
• Rummagene gene sets with description 01172024 ↗

  Figshare · 2024
  not yet assessed
• Rummagene gene sets with descriptions 01172024 ↗

  Figshare · 2024
  not yet assessed
• Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays ↗

  STAR Protocols · 2024 · PMID 39565691
  not yet assessed
• sc2DAT: workflow for targeting tumor subpopulations of single cells ↗

  Bioinformatics Advances · 2024 · PMID 41079221
  not yet assessed
• Enrichr-KG: bridging enrichment analysis across multiple libraries ↗

  Nucleic Acids Research · 2023 · PMID 37166973
  not yet assessed
• Proteogenomic insights suggest druggable pathways in endometrial carcinoma ↗

  Cancer Cell · 2023 · PMID 37567170
  not yet assessed
• Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis ↗

  Nature Cardiovascular Research · 2023 · PMID 37771373
  not yet assessed
• Toxicology knowledge graph for structural birth defects ↗

  Communications Medicine · 2023 · PMID 37460679
  not yet assessed
• lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs ↗

  Database · 2023 · PMID 36869839
  not yet assessed
• PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices ↗

  PeerJ · 2023 · PMID 36874981
  not yet assessed
• GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery ↗

  Nucleic Acids Research · 2023 · PMID 37166966
  not yet assessed
• Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells ↗

  Aging Cell · 2023 · PMID 37082798
  not yet assessed
• Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis ↗

  PeerJ · 2023 · PMID 37953774
  not yet assessed
• D2H2: diabetes data and hypothesis hub

  Bioinformatics Advances · 2023 · PMID 38107655
• Rummagene: Mining Gene Sets from Supporting Materials of PMC Publications ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Publisher Correction: Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis ↗

  Nature Cardiovascular Research · 2023 · PMID 38666036
  not yet assessed
• Connecting omics signatures and revealing biological mechanisms with iLINCS ↗

  Nature Communications · 2022 · PMID 35945222
  not yet assessed
• SigCom LINCS: data and metadata search engine for a million gene expression signatures ↗

  Nucleic Acids Research · 2022 · PMID 35524556
  not yet assessed
• DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules ↗

  BMC Bioinformatics · 2022 · PMID 35183110
  not yet assessed
• PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes ↗

  Cell stem cell · 2022 · PMID 35325615
  not yet assessed
• blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation ↗

  Bioinformatics · 2022 · PMID 35143610
  not yet assessed
• Getting Started with LINCS Datasets and Tools ↗

  Current Protocols · 2022 · PMID 35876555
  not yet assessed
• A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses ↗

  Communications Biology · 2022 · PMID 36207580
  not yet assessed
• Transforming L1000 profiles to RNA-seq-like profiles with deep learning ↗

  BMC Bioinformatics · 2022 · PMID 36100892
  not yet assessed
• Making Common Fund data more findable: catalyzing a data ecosystem ↗

  GigaScience · 2022 · PMID 36409836
  not yet assessed
• Gene set predictor for post-treatment Lyme disease ↗

  Cell Reports Medicine · 2022 · PMID 36384094
  not yet assessed
• Getting Started with the IDG KMC Datasets and Tools ↗

  Current Protocols · 2022 · PMID 35085427
  not yet assessed
• Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses ↗

  Aging Cell · 2022 · PMID 36111352
  not yet assessed
• Gene and drug landing page aggregator ↗

  Bioinformatics Advances · 2022 · PMID 35368424
  not yet assessed
• ReproTox-KG: Toxicology Knowledge Graph for Structural Birth Defects ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Hexyl Nayori ↗

  nmrXiv · 2022
  not yet assessed
• Project-1 ↗

  nmrXiv · 2022
  not yet assessed
• Hexyl Nayori[1] ↗

  nmrXiv · 2022
  not yet assessed
• Project-1 ↗

  nmrXiv · 2022
  not yet assessed
• Gene Set Knowledge Discovery with Enrichr ↗

  Current Protocols · 2021 · PMID 33780170
  not yet assessed
• KEA3: improved kinase enrichment analysis via data integration ↗

  Nucleic Acids Research · 2021 · PMID 34019655
  not yet assessed
• Recent Progress in Lyme Disease and Remaining Challenges ↗

  Frontiers in Medicine · 2021 · PMID 34485323
  not yet assessed
• Appyters: Turning Jupyter Notebooks into data-driven web apps ↗

  Patterns · 2021 · PMID 33748796
  not yet assessed
• Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation ↗

  Kidney International · 2021 · PMID 34634362
  not yet assessed
• Krüppel-like factor 6–mediated loss of BCAA catabolism contributes to kidney injury in mice and humans ↗

  Proceedings of the National Academy of Sciences · 2021 · PMID 34074766
  not yet assessed
• Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning ↗

  Database · 2021 · PMID 33787872
  not yet assessed
• Transcriptomic profiling of recessive dystrophic epidermolysis bullosa wounded skin highlights drug repurposing opportunities to improve wound healing ↗

  Experimental Dermatology · 2021 · PMID 34694680
  not yet assessed
• Transcriptome analysis of human dermal fibroblasts following red light phototherapy ↗

  Scientific Reports · 2021 · PMID 33795767
  not yet assessed
• Prioritizing Pain-Associated Targets with Machine Learning ↗

  Biochemistry · 2021 · PMID 33606503
  not yet assessed
• Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing ↗

  Frontiers in Immunology · 2021 · PMID 33763080
  not yet assessed
• An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions ↗

  Frontiers in Cell and Developmental Biology · 2021 · PMID 33816475
  not yet assessed
• A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Making Common Fund data more findable: Catalyzing a Data Ecosystem ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• PrismExp: Predicting Human Gene Function by Partitioning Massive RNA-seq Co-expression Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Publisher Correction: A systems approach identifies HIPK2 as a key regulator of kidney fibrosis ↗

  Nature Medicine · 2021 · PMID 34285421
  not yet assessed
• PPARdelta signaling activation improves metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Abstract 13468: Single-Cell Driven Drug Repositioning Approach Identifies a New Anti-Atherosclerotic Compound Targeting Myeloid Cells ↗

  Circulation · 2021
  not yet assessed
• CPTAC Pancancer Phosphoproteomics Kinase Enrichment Analysis with ProKAP Provides Insights into Immunogenic Signaling Pathways ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• The COVID-19 Drug and Gene Set Library ↗

  Patterns · 2020 · PMID 32838343
  not yet assessed
• Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells ↗

  The Journal of Immunology · 2020 · PMID 32948687
  not yet assessed
• Genetic driver mutations introduced in identical cell‐of‐origin in murine glioblastoma reveal distinct immune landscapes but similar response to checkpoint blockade ↗

  Glia · 2020 · PMID 32639068
  not yet assessed
• Interoperable RNA-Seq analysis in the cloud ↗

  Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · 2020 · PMID 32156561
  not yet assessed
• Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects ↗

  JACC Basic to Translational Science · 2020 · PMID 32368696
  not yet assessed
• piNET: a versatile web platform for downstream analysis and visualization of proteomics data ↗

  Nucleic Acids Research · 2020 · PMID 32469073
  not yet assessed
• Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease ↗

  Diabetes · 2020 · PMID 33067313
  not yet assessed
• Towards Intelligent Integration and Sharing of Stem Cell Research Data ↗

  Studies in health technology and informatics · 2020 · PMID 32604670
  not yet assessed
• Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment ↗

  Stem Cell Reports · 2020 · PMID 32243840
  not yet assessed
• Chemokine Signatures of Pathogen-Specific T Cells II: Memory T Cells in Acute and Chronic Infection ↗

  The Journal of Immunology · 2020 · PMID 32948682
  not yet assessed
• EnrichrBot: Twitter bot tracking tweets about human genes ↗

  Bioinformatics · 2020 · PMID 32277816
  not yet assessed
• GPR84: an immune response dial? ↗

  Nature Reviews Drug Discovery · 2020 · PMID 32494048
  not yet assessed
• Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• The COVID-19 Gene and Drug Set Library ↗

  Research Square · 2020 · PMID 32702729
  not yet assessed
• The COVID-19 Gene and Drug Set Library ↗

  SSRN Electronic Journal · 2020
  not yet assessed
• Chemokine Signatures Of Pathogen-Specific T Cells I: Effector T Cells ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• The COVID-19 Drug and Gene Set Library. Kuleshov et al ↗

  Data Archiving and Networked Services (DANS) · 2020
  not yet assessed
• Abstract 1313: Genomic and transcriptomic profiles of primary prostate cancer identify unique targets for therapeutic intervention ↗

  Cancer Research · 2020
  not yet assessed
• Connectivity mapping identifies BI-2536 as a potential drug to treat diabetic kidney disease ↗

  2020
  not yet assessed
• Connectivity mapping identifies BI-2536 as a potential drug to treat diabetic kidney disease ↗

  2020
  not yet assessed
• Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors ↗

  UNC Libraries · 2020
  not yet assessed
• ChEA3: transcription factor enrichment analysis by orthogonal omics integration ↗

  Nucleic Acids Research · 2019 · PMID 31114921
  not yet assessed
• Single-cell immune landscape of human atherosclerotic plaques ↗

  Nature Medicine · 2019 · PMID 31591603
  not yet assessed
• LINCS Data Portal 2.0: next generation access point for perturbation-response signatures ↗

  Nucleic Acids Research · 2019 · PMID 31701147
  not yet assessed
• A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines ↗

  Cell Systems · 2019 · PMID 31302153
  not yet assessed
• Dermal sheath contraction powers stem cell niche relocation during hair cycle regression ↗

  Science · 2019 · PMID 31857493
  not yet assessed
• Habenular TCF7L2 links nicotine addiction to diabetes ↗

  Nature · 2019 · PMID 31619789
  not yet assessed
• modEnrichr: a suite of gene set enrichment analysis tools for model organisms ↗

  Nucleic Acids Research · 2019 · PMID 31069376
  not yet assessed
• Predicting opioid dependence from electronic health records with machine learning ↗

  BioData Mining · 2019 · PMID 30728857
  not yet assessed
• Geneshot: search engine for ranking genes from arbitrary text queries ↗

  Nucleic Acids Research · 2019 · PMID 31114885
  not yet assessed
• Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells ↗

  Nature Cell Biology · 2019 · PMID 30988422
  not yet assessed
• FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources ↗

  Cell Systems · 2019 · PMID 31677972
  not yet assessed
• Connectivity Mapping: Methods and Applications ↗

  Annual Review of Biomedical Data Science · 2019
  not yet assessed
• Direct activation of PP2A for the treatment of tyrosine kinase inhibitor–resistant lung adenocarcinoma ↗

  JCI Insight · 2019 · PMID 30830869
  not yet assessed
• The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways ↗

  Scientific Data · 2019 · PMID 31672983
  not yet assessed
• Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• piNET: a versatile web platform for downstream analysis and visualization of proteomics data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• PKMYT1 is a computationally predicted target for kidney cancer ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Immune Profiling of Atherosclerotic Plaques Identifies Innate and Adaptive Dysregulations Associated with Ischemic Cerebrovascular Events ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• 2011 - ENGINEERING A HEMATOPOIETIC STEM CELL NICHE BY REVITALIZING MESENCHYMAL STEM CELLS ↗

  Experimental Hematology · 2019
  not yet assessed
• Engineering a Hematopoietic Stem Cell Niche By Revitalizing Mesenchymal Stem Cells with Five Transcription Factors ↗

  Blood · 2019
  not yet assessed
• Faculty Opinions recommendation of Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. ↗

  Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2019
  not yet assessed
• Faculty Opinions recommendation of Regularized Programming with the BOSQUE Language. ↗

  Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2019
  not yet assessed
• Faculty Opinions recommendation of Deep learning: new computational modelling techniques for genomics. ↗

  Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2019
  not yet assessed
• Massive mining of publicly available RNA-seq data from human and mouse ↗

  Nature Communications · 2018 · PMID 29636450
  not yet assessed
• Unexplored therapeutic opportunities in the human genome ↗

  Nature Reviews Drug Discovery · 2018 · PMID 29472638
  not yet assessed
• BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud ↗

  Cell Systems · 2018 · PMID 30447998
  not yet assessed
• eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks ↗

  Nucleic Acids Research · 2018 · PMID 29800326
  not yet assessed
• L1000FWD: fireworks visualization of drug-induced transcriptomic signatures ↗

  Bioinformatics · 2018 · PMID 29420694
  not yet assessed
• Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent ↗

  Developmental Cell · 2018 · PMID 30595537
  not yet assessed
• Mining data and metadata from the gene expression omnibus ↗

  Biophysical Reviews · 2018 · PMID 30594974
  not yet assessed
• SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling ↗

  Nature Communications · 2018 · PMID 30143629
  not yet assessed
• Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks ↗

  Science Signaling · 2018 · PMID 29789295
  not yet assessed
• Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease ↗

  Journal of the American Society of Nephrology · 2018 · PMID 30143559
  not yet assessed
• Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures ↗

  Bioinformatics · 2018 · PMID 30169739
  not yet assessed
• Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition ↗

  PLoS Computational Biology · 2018 · PMID 29293502
  not yet assessed
• Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming ↗

  Cell Reports · 2018 · PMID 30517869
  not yet assessed
• Effect of short-term liver X receptor activation on epidermal barrier features in mild to moderate atopic dermatitis ↗

  Annals of Allergy Asthma & Immunology · 2018 · PMID 29567358
  not yet assessed
• Temporal proteomic profiling of postnatal human cortical development ↗

  Translational Psychiatry · 2018 · PMID 30518843
  not yet assessed
• Far away from the lamppost ↗

  PLoS Biology · 2018 · PMID 30532236
  not yet assessed
• Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications ↗

  Stem Cell Research · 2018 · PMID 29936335
  not yet assessed
• Erratum: Unexplored therapeutic opportunities in the human genome ↗

  Nature Reviews Drug Discovery · 2018 · PMID 29567993
  not yet assessed
• Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center ↗

  Scientific Data · 2018 · PMID 29917015
  not yet assessed
• Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses ↗

  Scientific Data · 2018 · PMID 29485625
  not yet assessed
• BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Elysium: RNA-seq Alignment in the Cloud ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to its Formation and Is Progenitor Dependent ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• 1387 Identifying the key niche signals for hair follicle formation ↗

  Journal of Investigative Dermatology · 2018
  not yet assessed
• The Art of Connectivity Mapping ↗

  2018
  not yet assessed
• Cell-specific prediction and application of drug-induced gene expression .

  2018
  not yet assessed
• Fate Before Function: Specification of the Hair Follicle Niche Occurs Prior to Its Formation and is Progenitor Dependent ↗

  SSRN Electronic Journal · 2018
  not yet assessed
• The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations ↗

  Cell Systems · 2017 · PMID 29199020
  not yet assessed
• Differential cytokine contributions of perivascular haematopoietic stem cell niches ↗

  Nature Cell Biology · 2017 · PMID 28218906
  not yet assessed
• Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data ↗

  Nucleic Acids Research · 2017 · PMID 29140462
  not yet assessed
• Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth ↗

  Journal of Clinical Investigation · 2017 · PMID 28504649
  not yet assessed
• Complex systems biology ↗

  Journal of The Royal Society Interface · 2017 · PMID 28931638
  not yet assessed
• Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling ↗

  Nature Communications · 2017 · PMID 29084964
  not yet assessed
• Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age ↗

  Journal of Biomedical Informatics · 2017 · PMID 29113935
  not yet assessed
• Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis ↗

  Kidney International · 2017 · PMID 29102373
  not yet assessed
• Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop ↗

  Journal of Biomedical Informatics · 2017 · PMID 28501646
  not yet assessed
• Cell-specific prediction and application of drug-induced gene expression profiles ↗

  2017 · PMID 29218867
  not yet assessed
• Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data ↗

  Scientific Data · 2017 · PMID 28994825
  not yet assessed
• Massive Mining of Publicly Available RNA-seq Data from Human and Mouse ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Clustergrammer Lung Cancer PTM Case Study Data ↗

  Figshare · 2017
  not yet assessed
• Clustergrammer Kinase-Substrate Case Study Data ↗

  Figshare · 2017
  not yet assessed
• Clustergrammer Single Cell PBMC CyTOF Case Study Data ↗

  Figshare · 2017
  not yet assessed
• Abstract IA05: New methods and better theory for pre-clinical cancer pharmacogenomics ↗

  Cancer Research · 2017
  not yet assessed
• 862 Defining the molecular signature of the hair follicle dermal sheath and its functional requirement for hair cycle progression during catagen ↗

  Journal of Investigative Dermatology · 2017
  not yet assessed
• "Big Data Science with the BD2K-LINCS Data Coordination and Integration Center" MOOC Description, Retrieved from Coursera 2017-06-27

  2017
  not yet assessed
• Temporal proteomic profiling of postnatal human cortical development ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Clustergrammer Single Cell PBMC CyTOF Data ↗

  Figshare · 2017
  not yet assessed
• Clustergrammer Lung Cancer Case Study PTM Data ↗

  Figshare · 2017
  not yet assessed
• Enrichr: a comprehensive gene set enrichment analysis web server 2016 update ↗

  Nucleic Acids Research · 2016 · PMID 27141961
  not yet assessed
• The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins ↗

  Database · 2016 · PMID 27374120
  not yet assessed
• L1000CDS2: LINCS L1000 characteristic direction signatures search engine ↗

  npj Systems Biology and Applications · 2016 · PMID 28413689
  not yet assessed
• Pharos: Collating protein information to shed light on the druggable genome ↗

  Nucleic Acids Research · 2016 · PMID 27903890
  not yet assessed
• Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd ↗

  Nature Communications · 2016 · PMID 27667448
  not yet assessed
• Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration ↗

  Nature Neuroscience · 2016 · PMID 27526204
  not yet assessed
• Drug-induced adverse events prediction with the LINCS L1000 data ↗

  Bioinformatics · 2016 · PMID 27153606
  not yet assessed
• Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles ↗

  Cell Reports · 2016 · PMID 27009580
  not yet assessed
• Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain ↗

  eLife · 2016 · PMID 26894958
  not yet assessed
• Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning ↗

  Briefings in Bioinformatics · 2016 · PMID 28200013
  not yet assessed
• Krüppel–Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers ↗

  Journal of the American Society of Nephrology · 2016 · PMID 27288011
  not yet assessed
• Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production ↗

  Scientific Reports · 2016 · PMID 27226058
  not yet assessed
• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

  F1000Research · 2016 · PMID 27583132
  L1 74/100
• Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens ↗

  Frontiers in Molecular Neuroscience · 2016 · PMID 28066174
  not yet assessed
• Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma ↗

  Oncotarget · 2016 · PMID 26863628
  not yet assessed
• GEN3VA: aggregation and analysis of gene expression signatures from related studies ↗

  BMC Bioinformatics · 2016 · PMID 27846806
  not yet assessed
• Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd ↗

  LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) · 2016
  not yet assessed
• Clustergrammer: web-based heatmap visualization and analysis tool for high-dimensional biological data ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Abstract 788: Transcriptional landscape of drug response guides the design of potent and synergistic drug combinations ↗

  Cancer Research · 2016
  not yet assessed
• Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations ↗

  arXiv (Cornell University) · 2016
  not yet assessed
• Zika-RNAseq-Pipeline v0.1 ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2016
  not yet assessed
• 701 Signaling networks between stem cell precursors, transit amplifying progenitors, and their niche in developing hair follicles ↗

  Journal of Investigative Dermatology · 2016
  not yet assessed
• FAIR LINCS Data and Metadata powered by the CEDAR Framework ↗

  INDIGO (University of Illinois at Chicago) · 2016
  not yet assessed
• Community training and outreach activities of the BD2K-LINCS data coordination and integration center (DCIC) ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Cloud-based drag-and-drop scalable RNA sequencing pipeline ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• RNA-seq pipeline tutorial with an example of reprocessing data from a recent Zika virus study ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Predicting adverse cardiovascular events for tyrosine kinase inhibitors from molecular features ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Datasets2Tools: enriching DataMed with canned analyses ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Dashboard visualization and tool integration for Enrichr ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• GEN3VA: aggregation and analysis of gene expression signatures from related studies ↗

  Faculty of 1000 Research Ltd · 2016
  not yet assessed
• Fetal liver hematopoietic stem cell niches associate with portal vessels ↗

  Science · 2015 · PMID 26634440
  not yet assessed
• An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin ↗

  Developmental Cell · 2015 · PMID 26256211
  not yet assessed
• Krüppel-like factor 6 regulates mitochondrial function in the kidney ↗

  Journal of Clinical Investigation · 2015 · PMID 25689250
  not yet assessed
• A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis ↗

  PLoS Genetics · 2015 · PMID 26452208
  not yet assessed
• GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions ↗

  Bioinformatics · 2015 · PMID 25971742
  not yet assessed
• Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis ↗

  Molecular & Cellular Proteomics · 2015 · PMID 26149443
  not yet assessed
• Dynamics of the discovery process of protein-protein interactions from low content studies ↗

  BMC Systems Biology · 2015 · PMID 26048415
  not yet assessed
• Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool ↗

  2015 · PMID 26848405
  not yet assessed
• Reprint of “Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction” ↗

  Computational Biology and Chemistry · 2015 · PMID 26297300
  not yet assessed
• Publisher's Note: Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction ↗

  Computational Biology and Chemistry · 2015 · PMID 26101093
  not yet assessed
• Author response: Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain ↗

  2015
  not yet assessed
• Abstract PR16: Transcriptional landscape of drug response guides the design of specific and potent drug combinations ↗

  Cancer Research · 2015
  not yet assessed
• Abstract B20: Transcriptional landscape of drug response guides the design of specific and potent drug combinations ↗

  Molecular Cancer Therapeutics · 2015
  not yet assessed
• Abstract B1-28: GEO2Enrichr: A Google Chrome extension to extract gene sets from the Gene Expression Omnibus and analyze these lists for common biological functions ↗

  Cancer Research · 2015
  not yet assessed
• Abstract B1-25: Data integration for illuminating the druggable genome ↗

  Cancer Research · 2015
  not yet assessed
• Abstract SY10-04: Histone tail alterations in cellular senescence ↗

  Cancer Research · 2015
  not yet assessed
• Synaptic, transcriptional and chromatin genes disrupted in autism ↗

  Nature · 2014 · PMID 25363760
  not yet assessed
• LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures ↗

  Nucleic Acids Research · 2014 · PMID 24906883
  not yet assessed
• The characteristic direction: a geometrical approach to identify differentially expressed genes ↗

  BMC Bioinformatics · 2014 · PMID 24650281
  not yet assessed
• Histone H3.3 and its proteolytically processed form drive a cellular senescence programme ↗

  Nature Communications · 2014 · PMID 25394905
  not yet assessed
• DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics ↗

  Molecular Autism · 2014 · PMID 24602502
  not yet assessed
• Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells ↗

  PLoS Computational Biology · 2014 · PMID 25122140
  not yet assessed
• Lean Big Data integration in systems biology and systems pharmacology ↗

  Trends in Pharmacological Sciences · 2014 · PMID 25109570
  not yet assessed
• Interconnected Network Motifs Control Podocyte Morphology and Kidney Function ↗

  Science Signaling · 2014 · PMID 24497609
  not yet assessed
• B- <i>myb</i> is an essential regulator of hematopoietic stem cell and myeloid progenitor cell development ↗

  Proceedings of the National Academy of Sciences · 2014 · PMID 24516162
  not yet assessed
• Proteomics Analysis of the Non-Muscle Myosin Heavy Chain IIa-Enriched Actin-Myosin Complex Reveals Multiple Functions within the Podocyte ↗

  PLoS ONE · 2014 · PMID 24949636
  not yet assessed
• Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets ↗

  Bioinformatics · 2014 · PMID 25100688
  not yet assessed
• t 4 workshop report

  2014
  not yet assessed
• A blueprint of cell identity ↗

  Nature Biotechnology · 2014 · PMID 25299921
  not yet assessed
• A Systems Approach Identifies Essential FOXO3 Functions in Erythroblast Enucleation Process ↗

  Blood · 2014
  not yet assessed
• Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool ↗

  BMC Bioinformatics · 2013 · PMID 23586463
  not yet assessed
• Minimal Differentiation of Classical Monocytes as They Survey Steady-State Tissues and Transport Antigen to Lymph Nodes ↗

  Immunity · 2013 · PMID 24012416
  not yet assessed
• Induction of a Hemogenic Program in Mouse Fibroblasts ↗

  Cell stem cell · 2013 · PMID 23770078
  not yet assessed
• Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder ↗

  The American Journal of Human Genetics · 2013 · PMID 24094742
  not yet assessed
• ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells ↗

  Database · 2013 · PMID 23794736
  not yet assessed
• Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase ↗

  Journal of the American Society of Nephrology · 2013 · PMID 23559582
  not yet assessed
• Expression of HIV transgene aggravates kidney injury in diabetic mice ↗

  Kidney International · 2013 · PMID 23325078
  not yet assessed
• Network2Canvas: network visualization on a canvas with enrichment analysis ↗

  Bioinformatics · 2013 · PMID 23749960
  not yet assessed
• Systems Pharmacology Meets Predictive, Preventive, Personalized and Participatory Medicine ↗

  Pharmacogenomics · 2013 · PMID 23327571
  not yet assessed
• ELK1 Transcription Factor Linked to Dysregulated Striatal Mu Opioid Receptor Signaling Network and OPRM1 Polymorphism in Human Heroin Abusers ↗

  Biological Psychiatry · 2013 · PMID 23702428
  not yet assessed
• ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome ↗

  Lecture notes in computer science · 2013
  not yet assessed
• Metasignatures Identify Two Major Subtypes of Breast Cancer ↗

  CPT Pharmacometrics & Systems Pharmacology · 2013 · PMID 23836026
  not yet assessed
• Quantitative Approaches to Model Pluripotency and Differentiation in Stem Cells ↗

  2013
  not yet assessed
• RNA Sequencing Of Adult Bone Marrow Erythroid Populations Reveals Significant Transcriptional Deregulation In Foxo3-/- Mutant Cells ↗

  Blood · 2013
  not yet assessed
• Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages ↗

  Nature Immunology · 2012 · PMID 23023392
  not yet assessed
• Patterns and rates of exonic de novo mutations in autism spectrum disorders ↗

  Nature · 2012 · PMID 22495311
  not yet assessed
• A systems approach identifies HIPK2 as a key regulator of kidney fibrosis ↗

  Nature Medicine · 2012 · PMID 22406746
  not yet assessed
• Sox2 in the Dermal Papilla Niche Controls Hair Growth by Fine-Tuning BMP Signaling in Differentiating Hair Shaft Progenitors ↗

  Developmental Cell · 2012 · PMID 23153495
  not yet assessed
• Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity ↗

  Nature Cell Biology · 2012 · PMID 23103910
  not yet assessed
• Regulation of Embryonic and Induced Pluripotency by Aurora Kinase-p53 Signaling ↗

  Cell stem cell · 2012 · PMID 22862944
  not yet assessed
• Krüppel-like Factor 15 (KLF15) Is a Key Regulator of Podocyte Differentiation ↗

  Journal of Biological Chemistry · 2012 · PMID 22493483
  not yet assessed
• Receptor Heteromerization Expands the Repertoire of Cannabinoid Signaling in Rodent Neurons ↗

  PLoS ONE · 2012 · PMID 22235275
  not yet assessed
• 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 · 2012 · PMID 22499558
  not yet assessed
• Genes2FANs: connecting genes through functional association networks ↗

  BMC Bioinformatics · 2012 · PMID 22748121
  not yet assessed
• Activation of Alternate Prosurvival Pathways Accounts for Acquired Sunitinib Resistance in U87MG Glioma Xenografts ↗

  Journal of Pharmacology and Experimental Therapeutics · 2012 · PMID 22869928
  not yet assessed
• Sets2Networks: network inference from repeated observations of sets ↗

  BMC Systems Biology · 2012 · PMID 22824380
  not yet assessed
• Transforming Growth Factor β Signaling Controls Activities of Human Intestinal CD8+T Suppressor Cells ↗

  Gastroenterology · 2012 · PMID 23232296
  not yet assessed
• Colliding Dynamical Complex Network Models: Biological Attractors versus Attractors from Material Physics ↗

  Biophysical Journal · 2012 · PMID 23199907
  not yet assessed
• Network Pharmacology to Aid the Drug Discovery Process ↗

  2012
  not yet assessed
• New Frontiers of Network Analysis in Systems Biology ↗

  2012
  not yet assessed
• Biological and Quantitative Models for Stem Cell Self-Renewal and Differentiation ↗

  Elsevier eBooks · 2012
  not yet assessed
• Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer ↗

  2012
  not yet assessed
• Regulation of Primitive Erythroid Progenitor Development ↗

  Blood · 2012
  not yet assessed
• List of Contributors ↗

  Elsevier eBooks · 2012
  not yet assessed
• Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers ↗

  Bioinformatics · 2011 · PMID 22080467
  not yet assessed
• Oct4 links multiple epigenetic pathways to the pluripotency network ↗

  Cell Research · 2011 · PMID 22083510
  not yet assessed
• Introduction to Network Analysis in Systems Biology ↗

  Science Signaling · 2011 · PMID 21917719
  not yet assessed
• Systems biology of kidney diseases ↗

  Kidney International · 2011 · PMID 21881558
  not yet assessed
• Chronic Morphine Alters the Presynaptic Protein Profile: Identification of Novel Molecular Targets Using Proteomics and Network Analysis ↗

  PLoS ONE · 2011 · PMID 22043286
  not yet assessed
• Introduction to Statistical Methods to Analyze Large Data Sets: Principal Components Analysis ↗

  Science Signaling · 2011 · PMID 21917717
  not yet assessed
• Genes2WordCloud: a quick way to identify biological themes from gene lists and free text ↗

  Source Code for Biology and Medicine · 2011 · PMID 21995939
  not yet assessed
• Introduction to Statistical Methods for Analyzing Large Data Sets: Gene-Set Enrichment Analysis ↗

  Science Signaling · 2011 · PMID 21917718
  not yet assessed
• Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes ↗

  PLoS Computational Biology · 2011 · PMID 22219718
  not yet assessed
• Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format ↗

  Source Code for Biology and Medicine · 2011 · PMID 21418653
  not yet assessed
• FNV: light-weight flash-based network and pathway viewer ↗

  Bioinformatics · 2011 · PMID 21349871
  not yet assessed
• Primitive Erythroid Progenitors Are Regulated by Hypoxia and Display An Aerobic Glycolytic Metabolic Profile, ↗

  Blood · 2011
  not yet assessed
• Genes2Networks web interface ↗

  Figshare · 2011
  not yet assessed
• Mesenchymal and haematopoietic stem cells form a unique bone marrow niche ↗

  Nature · 2010 · PMID 20703299
  not yet assessed
• ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments ↗

  Bioinformatics · 2010 · PMID 20709693
  not yet assessed
• Global phosphorylation analysis of β-arrestin–mediated signaling downstream of a seven transmembrane receptor (7TMR) ↗

  Proceedings of the National Academy of Sciences · 2010 · PMID 20686112
  not yet assessed
• Systems Pharmacology of Arrhythmias ↗

  Science Signaling · 2010 · PMID 20407125
  not yet assessed
• Flotillin-Mediated Endocytic Events Dictate Cell Type-Specific Responses to Semaphorin 3A ↗

  Journal of Neuroscience · 2010 · PMID 21068336
  not yet assessed
• Lists2Networks: Integrated analysis of gene/protein lists ↗

  BMC Bioinformatics · 2010 · PMID 20152038
  not yet assessed
• SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells ↗

  BMC Systems Biology · 2010 · PMID 21176149
  not yet assessed
• Toward a complete <i>in silico</i> , multi‐layered embryonic stem cell regulatory network ↗

  WIREs Systems Biology and Medicine · 2010 · PMID 20890967
  not yet assessed
• Microdynamics and Criticality of Adaptive Regulatory Networks ↗

  Physical Review Letters · 2010 · PMID 20482087
  not yet assessed
• Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network ↗

  2010 · PMID 21552464
  not yet assessed
• Protein Kinase Target Discovery From Genome‐Wide Messenger RNA Expression Profiling ↗

  Mount Sinai Journal of Medicine A Journal of Translational and Personalized Medicine · 2010 · PMID 20687179
  not yet assessed
• Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair ↗

  Nature Genetics · 2009 · PMID 19684605
  not yet assessed
• Systems biology of stem cell fate and cellular reprogramming ↗

  Nature Reviews Molecular Cell Biology · 2009 · PMID 19738627
  not yet assessed
• Systems-level dynamic analyses of fate change in murine embryonic stem cells ↗

  Nature · 2009 · PMID 19924215
  not yet assessed
• KEA: kinase enrichment analysis ↗

  Bioinformatics · 2009 · PMID 19176546
  not yet assessed
• Systems approach to explore components and interactions in the presynapse ↗

  PROTEOMICS · 2009 · PMID 19562802
  not yet assessed
• GATE: software for the analysis and visualization of high-dimensional time series expression data ↗

  Bioinformatics · 2009 · PMID 19892805
  not yet assessed
• Neuro2A Differentiation by Gα _i/o Pathway ↗

  Science Signaling · 2009 · PMID 19155528
  not yet assessed
• SNAVI: Desktop application for analysis and visualization of large-scale signaling networks ↗

  BMC Systems Biology · 2009 · PMID 19154595
  not yet assessed
• Coordinated Regulation of Hematopoietic and Mesenchymal Stem Cells in a Bone Marrow Niche. ↗

  Blood · 2009
  not yet assessed
• Systems-level dynamic analyses of fate change in murine embryonic stem cells

  RePEc: Research Papers in Economics · 2009
  not yet assessed
• Microdynamics and Criticality in Evolving Random Graphs

  arXiv (Cornell University) · 2009
  not yet assessed
• Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget ↗

  Nature Precedings · 2009
  not yet assessed
• Design Logic of a Cannabinoid Receptor Signaling Network That Triggers Neurite Outgrowth ↗

  Science · 2008 · PMID 18487186
  not yet assessed
• Insights into the Organization of Biochemical Regulatory Networks Using Graph Theory Analyses ↗

  Journal of Biological Chemistry · 2008 · PMID 18940806
  not yet assessed
• Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks ↗

  Proceedings of the National Academy of Sciences · 2008 · PMID 19033453
  not yet assessed
• Retinoic Acid Utilizes CREB and USF1 in a Transcriptional Feed-Forward Loop in Order To Stimulate MKP1 Expression in Human Immunodeficiency Virus-Infected Podocytes ↗

  Molecular and Cellular Biology · 2008 · PMID 18625721
  not yet assessed
• Network integration and graph analysis in mammalian molecular systems biology ↗

  IET Systems Biology · 2008 · PMID 19045817
  not yet assessed
• Functions of Bifans in Context of Multiple Regulatory Motifs in Signaling Networks ↗

  Biophysical Journal · 2008 · PMID 18178648
  not yet assessed
• Proximity of intracellular regulatory networks to monotone systems ↗

  IET Systems Biology · 2008 · PMID 18537452
  not yet assessed
• Toward Stem Cell Systems Biology: From Molecules to Networks and Landscapes ↗

  Cold Spring Harbor Symposia on Quantitative Biology · 2008 · PMID 19329576
  not yet assessed
• Connecting Seed Lists of Mammalian Proteins Using Steiner Trees ↗

  Nature Precedings · 2008
  not yet assessed
• PubMedAlertMe—Standalone Windows-based PubMed SDI software application ↗

  Computers in Biology and Medicine · 2008 · PMID 18402930
  not yet assessed
• Functional atlas of the integrin adhesome ↗

  Nature Cell Biology · 2007 · PMID 17671451
  not yet assessed
• Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases ↗

  BMC Bioinformatics · 2007 · PMID 17916244
  not yet assessed
• Network analysis of FDA approved drugs and their targets ↗

  Mount Sinai Journal of Medicine A Journal of Translational and Personalized Medicine · 2007 · PMID 17516560
  not yet assessed
• AVIS: AJAX viewer of interactive signaling networks ↗

  Bioinformatics · 2007 · PMID 17855420
  not yet assessed
• Multiple Kinases and System Robustness: A Link Between Cdc37 and Genome Integrity ↗

  Cell Cycle · 2007 · PMID 18075309
  not yet assessed
• Connecting Seed Lists of Mammalian Proteins Using Steiner Trees ↗

  2018 52nd Asilomar Conference on Signals, Systems, and Computers · 2007
  not yet assessed
• Intracellular Regulatory Networks are close to Monotone Systems ↗

  Nature Precedings · 2007
  not yet assessed
• Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks ↗

  Nature Precedings · 2007
  not yet assessed
• Modeling Cell Signaling Networks ↗

  2007
  not yet assessed
• Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks ↗

  Nature Precedings · 2007
  not yet assessed
• The cognitive phenotype of Down syndrome: Insights from intracellular network analysis ↗

  NeuroRx · 2006 · PMID 16815222
  not yet assessed
• Topology of resultant networks shaped by evolutionary pressure ↗

  Physical Review E · 2006 · PMID 16906869
  not yet assessed
• From components to regulatory motifs in signalling networks ↗

  Briefings in Functional Genomics and Proteomics · 2006 · PMID 16769680
  not yet assessed
• The cognitive phenotype of Down syndrome: Insights from intracellular network analysis ↗

  Neurotherapeutics · 2006
  not yet assessed
• Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network ↗

  Science · 2005 · PMID 16099987
  not yet assessed
• Toward Predictive Models of Mammalian Cells ↗

  Annual Review of Biophysics and Biomolecular Structure · 2005 · PMID 15869393
  not yet assessed