Kimberly Glass

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 (1)

• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.⚑
  2024 L1 23/100 ⚑

1 assessed by us (0 reproduced) · 265 not yet assessed — every PubMed paper on record, linked below.

• Sex differences in gene regulation and its impact on cancer incidence ↗

  iScience · 2026
  not yet assessed
• HHIP’s dynamic role in epithelial wound healing reveals a potential mechanism of COPD susceptibility ↗

  Proceedings of the National Academy of Sciences · 2026 · PMID 39416045
  not yet assessed
• Joint clinical and molecular subtyping of COPD with variational autoencoders ↗

  Nature Communications · 2026 · PMID 38260473
  not yet assessed
• Integrative multi-omic analyses identify major axes of heterogeneity in chronic obstructive pulmonary disease and uncover their molecular contributors ↗

  medRxiv · 2026 · PMID 41646689
  not yet assessed
• Data for "Challenges and Opportunities in Single-Sample Network Modeling" ↗

  Open MIND · 2026
  not yet assessed
• Data for "Challenges and Opportunities in Single-Sample Network Modeling" ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2026
  not yet assessed
• Challenges and Opportunities in Single-Sample Network Modeling ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2026 · PMID 41867852
  not yet assessed
• An Alternatively Translated Isoform of <i>PPARG</i> Suggests AF-1 Domain Inhibition as an Insulin Sensitization Target ↗

  Diabetes · 2025 · PMID 39854214
  not yet assessed
• HHIP protein interactions in lung cells provide insight into COPD pathogenesis ↗

  Human Molecular Genetics · 2025 · PMID 39945347
  not yet assessed
• Multi-omics protein signaling networks identify sex-specific therapeutic candidates in lung adenocarcinoma ↗

  Biology of Sex Differences · 2025 · PMID 41024254
  not yet assessed
• Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 39975108
  not yet assessed
• miRNA-mRNA network analysis identifies PAX5 as a potential regulator of adaptive immune response in COPD ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 40654788
  not yet assessed
• &lt;b&gt;An alternatively translated isoform of &lt;/b&gt;&lt;b&gt;&lt;i&gt;PPARG&lt;/i&gt;&lt;/b&gt;&lt;b&gt; proposes AF-1 domain inhibition as an insulin sensitization target&lt;/b&gt; ↗

  2025
  not yet assessed
• &lt;b&gt;An alternatively translated isoform of &lt;/b&gt;&lt;b&gt;&lt;i&gt;PPARG&lt;/i&gt;&lt;/b&gt;&lt;b&gt; proposes AF-1 domain inhibition as an insulin sensitization target&lt;/b&gt; ↗

  2025
  not yet assessed
• Abstract 7478: Lung cancer gene regulatory networks reflect smoking history and age-related metabolic pathway alterations ↗

  Cancer Research · 2025
  not yet assessed
• HHIP's Dynamic Role in Epithelial Wound Healing Reveals a Potential Mechanism of COPD Susceptibility ↗

  American Journal of Respiratory and Critical Care Medicine · 2025
  not yet assessed
• miRNA-mRNA Network Analysis Identifies PAX5 as a Potential Regulator of Adaptive Immune Response in COPD ↗

  American Journal of Respiratory and Critical Care Medicine · 2025
  not yet assessed
• Identifying COPD Exacerbation Endotypes Using a Network Approach ↗

  American Journal of Respiratory and Critical Care Medicine · 2025
  not yet assessed
• Differential causal networks highlight sex-based differences in human tissues ↗

  Briefings in Bioinformatics · 2025 · PMID 40794949
  not yet assessed
• Sex differences in gene regulation and its impact on cancer incidence ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 41332599
  not yet assessed
• Current and future directions in network biology ↗

  Bioinformatics Advances · 2024 · PMID 39143982
  not yet assessed
• Mitigating off‐target effects of small RNAs: conventional approaches, network theory and artificial intelligence ↗

  British Journal of Pharmacology · 2024 · PMID 39293936
  not yet assessed
• Sex-Biased Regulation of Extracellular Matrix Genes in Chronic Obstructive Pulmonary Disease ↗

  American Journal of Respiratory Cell and Molecular Biology · 2024 · PMID 39102858
  not yet assessed
• The metabolic role of vitamin D in children’s neurodevelopment: a network study ↗

  Scientific Reports · 2024 · PMID 39043876
  not yet assessed
• Unlocking mitochondrial dysfunction-associated senescence (MiDAS) with NAD+ – A Boolean model of mitochondrial dynamics and cell cycle control ↗

  Translational Oncology · 2024 · PMID 39163758
  not yet assessed
• Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes in the COPDGene and ECLIPSE cohort studies ↗

  EBioMedicine · 2024 · PMID 39509750
  not yet assessed
• Using methylation data to improve transcription factor binding prediction ↗

  Epigenetics · 2024 · PMID 38300850
  not yet assessed
• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals⚑

  PLoS Computational Biology · 2024 · PMID 39418301
  L1 23/100 ⚑
• BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data ↗

  Lecture notes in computer science · 2024
  not yet assessed
• HHIP protein interactions in lung cells provide insight into COPD pathogenesis ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024 · PMID 38617310
  not yet assessed
• Gene Targeting in Disease Networks ↗

  UNC Libraries · 2024
  not yet assessed
• Discovering Joint Clinical and Molecular Subtypes of COPD With Variational Autoencoders ↗

  2024
  not yet assessed
• Polygenic and Transcriptional Risk Scores Identify Chronic Obstructive Pulmonary Disease Subtypes ↗

  2024
  not yet assessed
• The Mechanogenetic Role of microRNA in Asthmatic Bronchoconstriction ↗

  2024
  not yet assessed
• miRNA Network Modeling Identifies a Potential Role for PAX5 in COPD ↗

  2024
  not yet assessed
• Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes ↗

  medRxiv · 2024 · PMID 38826461
  not yet assessed
• The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks ↗

  Genome biology · 2023 · PMID 36894939
  not yet assessed
• Single-sample network modeling on omics data ↗

  BMC Biology · 2023 · PMID 38155351
  not yet assessed
• Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions ↗

  Nucleic Acids Research · 2023 · PMID 37953325
  not yet assessed
• Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data ↗

  Bioinformatics · 2023 · PMID 37802917
  not yet assessed
• Using Multi-Omic Data to Model Gene Regulatory Networks ↗

  2023
  not yet assessed
• Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO) ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023 · PMID 38014256
  not yet assessed
• Current and future directions in network biology ↗

  arXiv (Cornell University) · 2023
  not yet assessed
• The metabolic role of vitamin D in children’s neurodevelopment: a network study ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023 · PMID 37425858
  not yet assessed
• A Transcriptomic Signature of Mepolizumab Response in Eosinophilic Granulomatosis With Polyangiitis (EGPA) ↗

  2023
  not yet assessed
• Human extracellular sulfatases use a dual mechanism for regulation of growth factor interactions with heparan sulfate proteoglycans ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023 · PMID 38045270
  not yet assessed
• Unlocking Mitochondrial Dysfunction-Associated Senescence (MiDAS) with NAD ⁺ – a Boolean Model of Mitochondrial Dynamics and Cell Cycle Control ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023 · PMID 38187609
  not yet assessed
• Abstract 16835: Plasma Proteomics and Risk of Incident HFpEF and HFrEF: The Atherosclerosis Risk in Communities Study ↗

  Circulation · 2023
  not yet assessed
• Development and validation of enzyme replacement therapy for GM1 gangliosidosis ↗

  Molecular Genetics and Metabolism · 2023
  not yet assessed
• Data from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Figure S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Figure S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Table S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Table S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Figure S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Table S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Table S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Figure S2 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Activation of Adam12-SDC4 and CCL22-CCR4 Pathways in the Airway in Asthma ↗

  2023
  not yet assessed
• Network Medicine Approaches Reveal Sex-biased Regulation of Extracellular Matrix Pathway in COPD ↗

  2023
  not yet assessed
• Using Multi-omics Factor Analysis to Determine the Major Axes of Heterogeneity in Chronic Obstructive Pulmonary Disease ↗

  2023
  not yet assessed
• 284-OR: An Alternative Downstream Translational Start Site in PPARG Produces a Novel Protein That Rescues Loss-of-Function Mutations in Humans ↗

  Diabetes · 2023
  not yet assessed
• Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes ↗

  2023
  not yet assessed
• Abstract 16931: Network Analysis Identifies Partially Distinct Plasma Protein Associations Underlying HFpEF and HFrEF ↗

  Circulation · 2023
  not yet assessed
• Data from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  2023
  not yet assessed
• Nutrition state of science and dementia prevention: recommendations of the Nutrition for Dementia Prevention Working Group ↗

  The Lancet Healthy Longevity · 2022 · PMID 35821792
  not yet assessed
• Single Cell Transcriptomic Analysis Reveals Organ Specific Pericyte Markers and Identities ↗

  Frontiers in Cardiovascular Medicine · 2022 · PMID 35722109
  not yet assessed
• Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Respiratory Research · 2022 · PMID 35331221
  not yet assessed
• Multiplex genome editing of mammalian cells for producing recombinant heparin ↗

  Metabolic Engineering · 2022 · PMID 35038554
  not yet assessed
• An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks ↗

  Nature Methods · 2022 · PMID 35459940
  not yet assessed
• Transcriptional changes in human palate and skin healing ↗

  Wound Repair and Regeneration · 2022 · PMID 36571451
  not yet assessed
• ETV2 regulates PARP-1 binding protein to induce ER stress–mediated death in tuberin-deficient cells ↗

  Life Science Alliance · 2022 · PMID 35181635
  not yet assessed
• gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit ↗

  NAR Genomics and Bioinformatics · 2022 · PMID 35156023
  not yet assessed
• Predicting genotype-specific gene regulatory networks ↗

  Genome Research · 2022 · PMID 35193937
  not yet assessed
• The Network Zoo: a multilingual package for the inference and analysis of biological networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Using methylation data to improve transcription factor binding prediction ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Editorial: Applications and Methods in Genomic Networks ↗

  Frontiers in Genetics · 2022 · PMID 35754814
  not yet assessed
• Transcriptional changes in human palate and skin healing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Automated selection of changepoints using empirical <i>P</i>-values and trimming ↗

  JAMIA Open · 2022 · PMID 36325307
  not yet assessed
• Additional file 5 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 2 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 4 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 9 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 6 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 8 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 7 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• Additional file 3 of Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease ↗

  Figshare · 2022
  not yet assessed
• GRAND: a database of gene regulatory network models across human conditions ↗

  Nucleic Acids Research · 2021 · PMID 34508353
  not yet assessed
• Effects of novel SGLT2 inhibitors on cancer incidence in hyperglycemic patients: a meta-analysis of randomized clinical trials ↗

  Pharmacological Research · 2021 · PMID 34929299
  not yet assessed
• Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside ↗

  Clinical Epigenetics · 2021 · PMID 33785068
  not yet assessed
• Constructing gene regulatory networks using epigenetic data ↗

  npj Systems Biology and Applications · 2021 · PMID 34887443
  not yet assessed
• Gene Targeting in Disease Networks ↗

  Frontiers in Genetics · 2021 · PMID 33968133
  not yet assessed
• Longitudinal Association Between Muscle Loss and Mortality in Ever Smokers ↗

  CHEST Journal · 2021 · PMID 34785234
  not yet assessed
• Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells ↗

  Science Advances · 2021 · PMID 34301595
  not yet assessed
• Gene Regulatory Network Inference as Relaxed Graph Matching ↗

  Proceedings of the AAAI Conference on Artificial Intelligence · 2021
  not yet assessed
• Gene regulatory network inference as relaxed graph matching. ↗

  PubMed · 2021 · PMID 34707916
  not yet assessed
• Connecting COPD GWAS Genes: FAM13A Controls TGFβ2 Secretion by Modulating AP-3 Transport ↗

  American Journal of Respiratory Cell and Molecular Biology · 2021 · PMID 34166600
  not yet assessed
• GRAND: A database of gene regulatory network models across human conditions ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Reconstructing Sample-Specific Networks using LIONESS ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Predicting genotype-specific gene regulatory networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• ETV2 regulates PARP-1 binding protein to induce ER stress-mediated cell death in tuberin-deficient cells ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Gene targeting in disease networks ↗

  arXiv (Cornell University) · 2021
  not yet assessed
• Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues ↗

  Cell Reports · 2020 · PMID 32579922
  not yet assessed
• Molecular networks in Network Medicine: Development and applications ↗

  WIREs Systems Biology and Medicine · 2020 · PMID 32307915
  not yet assessed
• Robustness and lethality in multilayer biological molecular networks ↗

  Nature Communications · 2020 · PMID 33247151
  not yet assessed
• Epigenetics and pulmonary diseases in the horizon of precision medicine: a review ↗

  European Respiratory Journal · 2020 · PMID 33214212
  not yet assessed
• Integrated transcriptomic correlation network analysis identifies COPD molecular determinants ↗

  Scientific Reports · 2020 · PMID 32099002
  not yet assessed
• PUMA: PANDA Using MicroRNA Associations ↗

  Bioinformatics · 2020 · PMID 32860050
  not yet assessed
• Prediagnostic 25-Hydroxyvitamin D Concentrations in Relation to Tumor Molecular Alterations and Risk of Breast Cancer Recurrence ↗

  Cancer Epidemiology Biomarkers & Prevention · 2020 · PMID 32238406
  not yet assessed
• Using network science tools to identify novel diet patterns in prodromal dementia ↗

  Neurology · 2020 · PMID 32321763
  not yet assessed
• Early-Life Body Adiposity and the Breast Tumor Transcriptome ↗

  JNCI Journal of the National Cancer Institute · 2020 · PMID 33136151
  not yet assessed
• Low dose environmental radon exposure and breast tumor gene expression ↗

  BMC Cancer · 2020 · PMID 32723380
  not yet assessed
• Involvement of fine particulate matter exposure with gene expression pathways in breast tumor and adjacent-normal breast tissue ↗

  Environmental Research · 2020 · PMID 32668536
  not yet assessed
• Gene Regulatory Network Inference as Relaxed Graph Matching ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Constructing Gene Regulatory Networks using Epigenetic Data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Histone demethylome map reveals combinatorial gene regulatory functions in embryonic stem cells ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Abstract 6569: Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation ↗

  Cancer Research · 2020
  not yet assessed
• Aging and Apoptosis Genes Lose Outgoing Regulatory Network Connections in COPD ↗

  2020
  not yet assessed
• Abstract A85: Prediagnostic 25-hydroxyvitamin D concentrations in relation to tumor molecular alterations and risk of breast cancer recurrence ↗

  Cancer Immunology Research · 2020
  not yet assessed
• Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Transcription Factor Binding] ↗

  Harvard Dataverse · 2020
  not yet assessed
• Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Histone Modification] ↗

  Harvard Dataverse · 2020
  not yet assessed
• Network Medicine in the Age of Biomedical Big Data ↗

  Frontiers in Genetics · 2019 · PMID 31031797
  not yet assessed
• RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD ↗

  Respiratory Research · 2019 · PMID 30940135
  not yet assessed
• Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection ↗

  Scientific Reports · 2019 · PMID 31554845
  not yet assessed
• Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization ↗

  Epigenetics · 2019 · PMID 30876376
  not yet assessed
• lionessR: single sample network inference in R ↗

  BMC Cancer · 2019 · PMID 31653243
  not yet assessed
• Genome-Wide Association Study for Urinary and Fecal Incontinence in Women ↗

  The Journal of Urology · 2019 · PMID 31729902
  not yet assessed
• New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs ↗

  Scientific Reports · 2019 · PMID 30837613
  not yet assessed
• TFutils: Data structures for transcription factor bioinformatics ↗

  F1000Research · 2019 · PMID 31297189
  not yet assessed
• The periphery and the core properties explain the omnigenic model in the human interactome ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• lionessR: single-sample network reconstruction in R ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  Cancer Research · 2019 · PMID 30987980
  not yet assessed
• Integrated transcriptomic correlation network analysis identifies COPD molecular determinants ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• PUMA: PANDA Using MicroRNA Associations ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Integrating epigenetics to construct gene regulatory networks

  Bulletin of the American Physical Society · 2019
  not yet assessed
• Network Medicine in the age of biomedical big data ↗

  arXiv (Cornell University) · 2019
  not yet assessed
• Abstract 2928: New insight into signaling contexts for the administration of the imipridone ONC201 to prostate cancer cells ↗

  Tumor Biology · 2019
  not yet assessed
• Identifying Gene Regulatory Networks of TREM-1 Response in Asthma ↗

  2019
  not yet assessed
• Prioritizing GWAS SNPs to Guide Functional Genomics of Human Lung Disease ↗

  2019
  not yet assessed
• Precision VISSTA: Machine Learning Prediction and Inference for Bring-Your-Own-Device (BYOD) mHealth Data.

  AMIA · 2019
  not yet assessed
• Precision VISSTA: Bring-Your-Own-Device (BYOD) mHealth Data for Precision Health.

  AMIA · 2019
  not yet assessed
• Abstract 2928: New insight into signaling contexts for the administration of the imipridone ONC201 to prostate cancer cells ↗

  Cancer Research · 2019
  not yet assessed
• TFutils: Data structures for transcription factor bioinformatics ↗

  F1000Research · 2019
  not yet assessed
• Additional file 3: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD ↗

  Figshare · 2019
  not yet assessed
• Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization ↗

  Figshare · 2019
  not yet assessed
• Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization ↗

  Figshare · 2019
  not yet assessed
• Referee report. For: Enhancing gene set enrichment using networks [version 1; referees: 1 approved] ↗

  Faculty of 1000 Research Ltd · 2019
  not yet assessed
• Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism ↗

  Cancer Research · 2018 · PMID 30275053
  not yet assessed
• Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci ↗

  American Journal of Respiratory and Critical Care Medicine · 2018 · PMID 29313708
  not yet assessed
• Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease ↗

  Human Genomics · 2018 · PMID 29335020
  not yet assessed
• A Network Analysis of Biomarkers for Type 2 Diabetes ↗

  Diabetes · 2018 · PMID 30409783
  not yet assessed
• Estimating Sample-Specific Regulatory Networks ↗

  iScience · 2018 · PMID 30981959
  not yet assessed
• Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke ↗

  Scientific Reports · 2018 · PMID 30143676
  not yet assessed
• Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism processes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Constructing Gene Regulatory Networks with Epigenetic data using Message-Passing

  Research in Computational Molecular Biology · 2018
  not yet assessed
• New Statistical Methods for Constructing Robust Differential Correlation Networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Abstract 839: Treatment and signaling contexts for the application of the imipridone ONC201 to prostate cancer cells ↗

  Cancer Research · 2018
  not yet assessed
• Signaling contexts for utilizing the imipridone ONC201 in prostate cancer. ↗

  European Urology Supplements · 2018
  not yet assessed
• P1‐591: USING NETWORK SCIENCE TOOLS TO IDENTIFY NOVEL DIET PATTERNS IN PRODROMAL DEMENTIA: THE THREE‐CITY STUDY ↗

  Alzheimer s & Dementia · 2018
  not yet assessed
• Mirna Gene Regulatory Networks For 38 Human Tissues ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2018
  not yet assessed
• Mirna Gene Regulatory Networks For 38 Human Tissues ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2018
  not yet assessed
• Referee report. For: aMatReader: Importing adjacency matrices via Cytoscape Automation [version 1; referees: 2 approved] ↗

  Faculty of 1000 Research Ltd · 2018
  not yet assessed
• Referee report. For: aMatReader: Importing adjacency matrices via Cytoscape Automation [version 2; referees: 2 approved] ↗

  Faculty of 1000 Research Ltd · 2018
  not yet assessed
• Understanding Tissue-Specific Gene Regulation ↗

  Cell Reports · 2017 · PMID 29069589
  not yet assessed
• Exploring regulation in tissues with eQTL networks ↗

  Proceedings of the National Academy of Sciences · 2017 · PMID 28851834
  not yet assessed
• Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue ↗

  Scientific Reports · 2017 · PMID 28287180
  not yet assessed
• Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  BMC Bioinformatics · 2017 · PMID 28974199
  not yet assessed
• Regulatory network changes between cell lines and their tissues of origin ↗

  BMC Genomics · 2017 · PMID 28899340
  not yet assessed
• Multi-scale chromatin state annotation using a hierarchical hidden Markov model ↗

  Nature Communications · 2017 · PMID 28387224
  not yet assessed
• Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation ↗

  Journal of Molecular and Cellular Cardiology · 2017 · PMID 29291394
  not yet assessed
• Transcriptomic Analysis of Lung Tissue from Cigarette Smoke–Induced Emphysema Murine Models and Human Chronic Obstructive Pulmonary Disease Show Shared and Distinct Pathways ↗

  American Journal of Respiratory Cell and Molecular Biology · 2017 · PMID 28248572
  not yet assessed
• Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma ↗

  Journal of Allergy and Clinical Immunology · 2017 · PMID 28736268
  not yet assessed
• Sex-Based Genetic Association Study Identifies <i>CELSR1</i> as a Possible Chronic Obstructive Pulmonary Disease Risk Locus among Women ↗

  American Journal of Respiratory Cell and Molecular Biology · 2017 · PMID 27854507
  not yet assessed
• Estimating gene regulatory networks with pandaR ↗

  Bioinformatics · 2017 · PMID 28334344
  not yet assessed
• Estimating drivers of cell state transitions using gene regulatory network models ↗

  BMC Systems Biology · 2017 · PMID 29237467
  not yet assessed
• Biomarker correlation network in colorectal carcinoma by tumor anatomic location ↗

  BMC Bioinformatics · 2017 · PMID 28623901
  not yet assessed
• Understanding Tissue-specific Gene Regulation ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Gene Regulatory Networks For 38 Human Tissues ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2017
  not yet assessed
• Multi-scale chromatin state annotation using a hierarchical hidden Markov model

  DSpace@MIT (Massachusetts Institute of Technology) · 2017
  not yet assessed
• Additional file 5: Table S1. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Gene Regulatory Networks For 38 Human Tissues ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2017
  not yet assessed
• Additional file 8: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 5: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 4: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 9: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 11: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 7: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 3: Figure S2. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 6: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 13: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 1: of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 3: Figure S2. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 3: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 7: Figure S5. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 2: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 3: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 6: Figure S4. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 10: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 2: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 2: Figure S1. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 1: of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 6: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 10: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 13: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 6: Figure S4. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 12: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 7: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 1: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 2: Figure S1. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 1: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 7: Figure S5. of Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  Figshare · 2017
  not yet assessed
• Additional file 12: of Regulatory network changes between cell lines and their tissues of origin ↗

  Figshare · 2017
  not yet assessed
• Additional file 4: Table S1. of Biomarker correlation network in colorectal carcinoma by tumor anatomic location ↗

  Figshare · 2017
  not yet assessed
• Additional file 4: Table S1. of Biomarker correlation network in colorectal carcinoma by tumor anatomic location ↗

  Figshare · 2017
  not yet assessed
• Mitochondrial iron chelation ameliorates cigarette smoke–induced bronchitis and emphysema in mice ↗

  Nature Medicine · 2016 · PMID 26752519
  not yet assessed
• DNA methylation profiling in human lung tissue identifies genes associated with COPD ↗

  Epigenetics · 2016 · PMID 27564456
  not yet assessed
• COPD subtypes identified by network-based clustering of blood gene expression ↗

  Genomics · 2016 · PMID 26773458
  not yet assessed
• Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa ↗

  Genomics · 2016 · PMID 27524493
  not yet assessed
• Sexual dimorphism in gene expression and regulatory networks across human tissues ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• PyPanda: a Python package for gene regulatory network reconstruction ↗

  Bioinformatics · 2016 · PMID 27402905
  not yet assessed
• Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• A network-based approach to eQTL interpretation and SNP functional characterization ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• Transcriptional landscape of cell lines and their tissues of origin ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• Estimating Drivers of Cell State Transitions Using Gene Regulatory Network Models ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• Exploring the role of inflammation in ETV1-expressing prostate tumours ↗

  European Journal of Cancer · 2016
  not yet assessed
• DNA methylation profiling in human lung tissue identifies genes associated with COPD ↗

  Figshare · 2016
  not yet assessed
• Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions ↗

  Molecular Cell · 2015 · PMID 25578878
  not yet assessed
• A network model for angiogenesis in ovarian cancer ↗

  BMC Bioinformatics · 2015 · PMID 25888305
  not yet assessed
• Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring ↗

  Genome Medicine · 2015 · PMID 25763110
  not yet assessed
• Finding New Order in Biological Functions from the Network Structure of Gene Annotations ↗

  PLoS Computational Biology · 2015 · PMID 26588252
  not yet assessed
• Student engagement and affordances for interaction with diverse peers: A network analysis. ↗

  Journal of Diversity in Higher Education · 2015
  not yet assessed
• High performance computing of gene regulatory networks using a message-passing model ↗

  2015
  not yet assessed
• Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer ↗

  Cancer Research · 2015
  not yet assessed
• Diet‐induced Weight Loss Changes in Gene Regulatory Networks in the Rectum: Network Analysis as a Compliment to Traditional Gene Expression Analysis ↗

  The FASEB Journal · 2015
  not yet assessed
• Mitophagy-dependent necroptosis contributes to the pathogenesis of COPD ↗

  Journal of Clinical Investigation · 2014 · PMID 25083992
  not yet assessed
• Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets ↗

  Scientific Reports · 2014 · PMID 24569707
  not yet assessed
• Sexually-dimorphic targeting of functionally-related genes in COPD ↗

  BMC Systems Biology · 2014 · PMID 25431000
  not yet assessed
• Developmental Control of Polycomb Subunit Composition Mediates a Switch to Non-Canonical Functions during Hematopoiesis ↗

  Blood · 2014
  not yet assessed
• Passing Messages between Biological Networks to Refine Predicted Interactions ↗

  PLoS ONE · 2013 · PMID 23741402
  not yet assessed
• KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors ↗

  Cell · 2013 · PMID 23871696
  not yet assessed
• Combinatorial Recruitment of CREB, C/EBPβ and c-Jun Determines Activation of Promoters upon Keratinocyte Differentiation ↗

  PLoS ONE · 2013 · PMID 24244291
  not yet assessed
• ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients ↗

  Genes & Development · 2013 · PMID 23512661
  not yet assessed
• Correction: Combinatorial Recruitment of CREB, C/EBPβ and c-Jun Determines Activation of Promoters upon Keratinocyte Differentiation ↗

  PLoS ONE · 2013
  not yet assessed
• Abstract 5393: ETV1 directs androgen metabolism and confers aggressive prostate cancer in engineered mice and patients. ↗

  Cancer Research · 2013
  not yet assessed
• Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis ↗

  Developmental Cell · 2012 · PMID 23041383
  not yet assessed
• Implications of functional similarity for gene regulatory interactions ↗

  Journal of The Royal Society Interface · 2012 · PMID 22298814
  not yet assessed
• Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets ↗

  arXiv (Cornell University) · 2012
  not yet assessed
• An Alternate Method for Organizing Biological Functions using Gene Annotation Networks

  arXiv (Cornell University) · 2012
  not yet assessed
• Abstract 2965: ERG and ETV1 regulate a common transcriptional network in prostate cells but in an opposite fashion ↗

  Cancer Research · 2012
  not yet assessed
• Genomic Determinants of Human Fetal and Adult Erythroid Gene Expression ↗

  Blood · 2012
  not yet assessed
• Finding New Order in Biological Functions from the Network Structure of Gene Annotations ↗

  arXiv (Cornell University) · 2012
  not yet assessed
• Annotation Enrichment Analysis: An Alternative Method for Evaluating the\n Functional Properties of Gene Sets ↗

  arXiv (Cornell University) · 2012
  not yet assessed
• Suppression of the C/EBP family of transcription factors in adipose tissue causes lipodystrophy ↗

  Journal of Molecular Endocrinology · 2011 · PMID 21321096
  not yet assessed
• Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine ↗

  Lab on a Chip · 2011 · PMID 22139143
  not yet assessed
• CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes ↗

  Proceedings of the National Academy of Sciences · 2010 · PMID 21059933
  not yet assessed
• Patterns and complexity in biological systems: a study of sequence structure and ontology-based networks

  2010
  not yet assessed
• A new function for methyl CpG: Creating a C/EBPα binding site &amp; mediating tissue‐specific gene expression ↗

  The FASEB Journal · 2010
  not yet assessed
• All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues ↗

  BMC Genomics · 2008 · PMID 18252004
  not yet assessed
• Detecting cooperative sequences in the binding of RNA Polymerase-II

  Bulletin of the American Physical Society · 2008
  not yet assessed
• Relating Promoter Sequences to the Proteins that Bind to Them: A Comparison Study.

  Bulletin of the American Physical Society · 2007
  not yet assessed
• Lactate dehydrogenase activity changes during peri-implantation.

  Transactions of the Illinois State Academy of Science · 1990
  not yet assessed
• [Model studies on blood flow relations on the semilunar valves of the heart]. ↗

  PubMed · 1961 · PMID 13705946
  not yet assessed