Footprint-based functional analysis of multiomic data

• Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression

  2025 Molecular Systems Biology article Medicine Chronic Kidney Disease and Diabetes Open access

  11

  citations
• Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion

  2024 iScience article Medicine Cancer Immunotherapy and Biomarkers Open access

  16

  citations
• Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access

  0

  citations
• Using a Network-Based Analysis Approach to Investigate the Involvement of S. aureus in the Pathogenesis of Granulomatosis with Polyangiitis

  2023 International Journal of Molecular Sciences article Medicine Vasculitis and related conditions Open access

  1

  citations
• Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment

  2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access

  226

  citations
• COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

  2021 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  105

  citations
• Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury

  2021 Toxicology Letters article Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access

  4

  citations
• New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids

  2021 Archives of Toxicology article Medicine Colorectal Cancer Treatments and Studies Open access

  57

  citations
• Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Pharmacology, Toxicology and Pharmaceutics Drug-Induced Hepatotoxicity and Protection Open access

  0

  citations
• Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses

  2021 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  156

  citations
• Why do pathway methods work better than they should?

  2020 FEBS Letters article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  38

  citations
• COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  11

  citations
• Big Data Approaches in Heart Failure Research

  2020 Current Heart Failure Reports article Medicine Heart Failure Treatment and Management Open access

  22

  citations
• Why do pathway methods work better than they should?

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  3

  citations
• Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  16

  citations
• Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

  2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  367

  citations

16 results