Passing Messages between Biological Networks to Refine Predicted Interactions

• Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data

  2024 Nature Computational Science article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  19

  citations
• Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data

  2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access

  12

  citations
• Heterogeneity in the gene regulatory landscape of leiomyosarcoma

  2023 NAR Cancer article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  9

  citations
• The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

  2023 Genome biology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  56

  citations
• WITHDRAWN: Exposure to an enriched environment improves colonic epithelial barrier integrity and attenuates mouse experimental colitis by modulating a Myc-driven gene regulatory network

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Inflammatory Bowel Disease Open access

  0

  citations
• Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  2

  citations
• The Network Zoo: a multilingual package for the inference and analysis of biological networks

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  1

  citations
• Heterogeneity in the gene regulatory landscape of leiomyosarcoma

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Sarcoma Diagnosis and Treatment Open access

  3

  citations
• gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit

  2022 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent

  8

  citations
• Reconstructing Sample-Specific Networks using LIONESS

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  3

  citations
• GRAND: a database of gene regulatory network models across human conditions

  2021 Nucleic Acids Research article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent

  102

  citations
• Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme

  2021 Cancer Research article Medicine Glioma Diagnosis and Treatment Open access

  31

  citations
• gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  2

  citations
• GRAND: A database of gene regulatory network models across human conditions

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  8

  citations
• Regulation of PD1 signaling is associated with prognosis in glioblastoma multiforme

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Glioma Diagnosis and Treatment Open access

  4

  citations
• Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks

  2021 Frontiers in Genetics article Agricultural and Biological Sciences Plant Molecular Biology Research Open access

  31

  citations

16 results