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Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 14, p. 8100, doi. 10.1093/nar/gkae552
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- Publication type:
- Article
Molecular causality in the advent of foundation models.
- Published in:
- Molecular Systems Biology, 2024, v. 20, n. 8, p. 848, doi. 10.1038/s44320-024-00041-w
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- Publication type:
- Article
A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens.
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- Clinical Proteomics, 2024, v. 21, n. 1, p. 1, doi. 10.1186/s12014-024-09501-9
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- Article
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions.
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- Briefings in Bioinformatics, 2024, v. 25, n. 4, p. 1, doi. 10.1093/bib/bbae347
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- Publication type:
- Article
DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48868-z
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- Publication type:
- Article
Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition.
- Published in:
- Molecular Systems Biology, 2024, v. 20, n. 4, p. 458, doi. 10.1038/s44320-024-00025-w
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- Publication type:
- Article
A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury.
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- Toxicological Sciences, 2024, v. 198, n. 1, p. 14, doi. 10.1093/toxsci/kfad121
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- Article
Profiling the heterogeneity of colorectal cancer consensus molecular subtypes using spatial transcriptomics.
- Published in:
- NPJ Precision Oncology, 2024, v. 8, n. 1, p. 1, doi. 10.1038/s41698-023-00488-4
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- Publication type:
- Article
Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44117-x
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- Publication type:
- Article
Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.
- Published in:
- eLife, 2023, p. 1, doi. 10.7554/eLife.93161
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- Publication type:
- Article
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities.
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- Nucleic Acids Research, 2023, v. 51, n. 20, p. 10934, doi. 10.1093/nar/gkad841
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- Publication type:
- Article
Enablers and challenges of spatial omics, a melting pot of technologies.
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- Molecular Systems Biology, 2023, v. 19, n. 11, p. 1, doi. 10.15252/msb.202110571
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- Publication type:
- Article
A network medicine approach to study comorbidities in heart failure with preserved ejection fraction.
- Published in:
- BMC Medicine, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12916-023-02922-7
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- Publication type:
- Article
Single‐cell biology: what does the future hold?
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- Molecular Systems Biology, 2023, v. 19, n. 7, p. 1, doi. 10.15252/msb.202311799
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- Publication type:
- Article
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.
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- Molecular Systems Biology, 2023, v. 19, n. 3, p. 1, doi. 10.15252/msb.202110631
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- Publication type:
- Article
Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.
- Published in:
- Clinical & Translational Medicine, 2023, v. 13, n. 2, p. 1, doi. 10.1002/ctm2.1179
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- Publication type:
- Article
A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets.
- Published in:
- Nature Protocols, 2022, v. 17, n. 12, p. 2920, doi. 10.1038/s41596-022-00740-4
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- Publication type:
- Article
Cross-regional homeostatic and reactive glial signatures in multiple sclerosis.
- Published in:
- Acta Neuropathologica, 2022, v. 144, n. 5, p. 987, doi. 10.1007/s00401-022-02497-2
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- Publication type:
- Article
Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31312-5
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- Publication type:
- Article
Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks.
- Published in:
- Molecular Systems Biology, 2022, v. 18, n. 7, p. 1, doi. 10.15252/msb.202211036
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- Publication type:
- Article
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30755-0
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- Publication type:
- Article
Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes.
- Published in:
- eLife, 2022, p. 1, doi. 10.7554/eLife.74391
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- Publication type:
- Article
Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways.
- Published in:
- NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00224-x
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- Publication type:
- Article
Patient-specific Boolean models of signalling networks guide personalised treatments.
- Published in:
- eLife, 2022, p. 1, doi. 10.7554/eLife.72626
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- Publication type:
- Article
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02663-5
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- Publication type:
- Article
Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010021
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- Article
FUNKI: interactive functional footprint-based analysis of omics data.
- Published in:
- Bioinformatics, 2022, v. 38, n. 7, p. 2075, doi. 10.1093/bioinformatics/btac055
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- Publication type:
- Article
Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signalling.
- Published in:
- Cardiovascular Research, 2022, v. 118, n. 5, p. 1232, doi. 10.1093/cvr/cvab152
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- Publication type:
- Article
Experimental and computational technologies to dissect the kidney at the single-cell level.
- Published in:
- Nephrology Dialysis Transplantation, 2022, v. 37, n. 4, p. 628, doi. 10.1093/ndt/gfaa233
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- Publication type:
- Article
The spatial transcriptomic landscape of the healing mouse intestine following damage.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28497-0
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- Publication type:
- Article
decoupleR: ensemble of computational methods to infer biological activities from omics data.
- Published in:
- Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbac016
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- Publication type:
- Article
The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment.
- Published in:
- Archives of Toxicology, 2021, v. 95, n. 12, p. 3745, doi. 10.1007/s00204-021-03141-w
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- Publication type:
- Article
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.
- Published in:
- Bioinformatics, 2021, v. 37, n. 21, p. 3702, doi. 10.1093/bioinformatics/btab229
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- Publication type:
- Article
Systems approach reveals distinct and shared signaling networks of the four PGE<sub>2</sub> receptors in T cells.
- Published in:
- Science Signaling, 2021, v. 14, n. 703, p. 1, doi. 10.1126/scisignal.abc8579
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- Article
Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd.
- Published in:
- Molecular Systems Biology, 2021, v. 17, n. 10, p. 1, doi. 10.15252/msb.202110402
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- Publication type:
- Article
How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade?
- Published in:
- Seminars in Immunopathology, 2021, v. 43, n. 5, p. 739, doi. 10.1007/s00281-021-00847-y
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- Publication type:
- Article
Correction to: How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade?
- Published in:
- 2021
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- Publication type:
- Correction Notice
Reusability and composability in process description maps: RAS–RAF–MEK–ERK signalling.
- Published in:
- Briefings in Bioinformatics, 2021, v. 22, n. 5, p. 1, doi. 10.1093/bib/bbab103
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- Publication type:
- Article
New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids.
- Published in:
- Archives of Toxicology, 2021, v. 95, n. 8, p. 2691, doi. 10.1007/s00204-021-03092-2
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- Publication type:
- Article
Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis.
- Published in:
- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00925-8
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- Publication type:
- Article
A comprehensive database for integrated analysis of omics data in autoimmune diseases.
- Published in:
- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04268-4
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- Publication type:
- Article
Consensus Transcriptional Landscape of Human End-Stage Heart Failure.
- Published in:
- 2021
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- Publication type:
- journal article
Transcription Factor Activity Inference in Systemic Lupus Erythematosus.
- Published in:
- Life (2075-1729), 2021, v. 11, n. 4, p. 299, doi. 10.3390/life11040299
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- Publication type:
- Article
Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
- Published in:
- Briefings in Bioinformatics, 2021, v. 22, n. 2, p. 1848, doi. 10.1093/bib/bbaa046
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- Publication type:
- Article
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis.
- Published in:
- Molecular Systems Biology, 2021, v. 17, n. 3, p. 1, doi. 10.15252/msb.20209923
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- Publication type:
- Article
Norepinephrine promotes triglyceride storage in macrophages via beta2‐adrenergic receptor activation.
- Published in:
- FASEB Journal, 2021, v. 35, n. 2, p. 1, doi. 10.1096/fj.202001101R
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- Article
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses.
- Published in:
- Molecular Systems Biology, 2021, v. 17, n. 1, p. 1, doi. 10.15252/msb.20209730
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- Publication type:
- Article
A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates.
- Published in:
- eLife, 2020, p. 1, doi. 10.7554/eLife.60352
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- Publication type:
- Article
Why do pathway methods work better than they should?
- Published in:
- FEBS Letters, 2020, v. 594, n. 24, p. 4189, doi. 10.1002/1873-3468.14011
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- Publication type:
- Article
Converting networks to predictive logic models from perturbation signalling data with CellNOpt.
- Published in:
- Bioinformatics, 2020, v. 36, n. 16, p. 4523, doi. 10.1093/bioinformatics/btaa561
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- Publication type:
- Article