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Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-36549-2
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scReClassify: post hoc cell type classification of single-cell rNA-seq data.
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- BMC Genomics, 2019, v. 20, n. 9, p. 1, doi. 10.1186/s12864-019-6305-x
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- Article
Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate.
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- Biochemical Journal, 2022, v. 479, n. 11, p. 1237, doi. 10.1042/BCJ20220153
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- Article
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac023
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Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance.
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- eLife, 2018, p. 1, doi. 10.7554/eLife.32111
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Enhanced structure and function of human pluripotent stem cell‐derived beta‐cells cultured on extracellular matrix.
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- Stem Cells Translational Medicine, 2021, v. 10, n. 3, p. 492, doi. 10.1002/sctm.20-0224
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- Article
A benchmark study of simulation methods for single-cell RNA sequencing data.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27130-w
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- Article
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25210-5
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Interpretable deep learning in single-cell omics.
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- Bioinformatics, 2024, v. 40, n. 6, p. 1, doi. 10.1093/bioinformatics/btae374
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Ensemble deep learning of embeddings for clustering multimodal single-cell omics data.
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- Bioinformatics, 2023, v. 39, n. 6, p. 1, doi. 10.1093/bioinformatics/btad382
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scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction.
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- Bioinformatics, 2022, v. 38, n. 20, p. 4745, doi. 10.1093/bioinformatics/btac590
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Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities.
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- Bioinformatics, 2022, v. 38, n. 7, p. 1956, doi. 10.1093/bioinformatics/btac015
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Evaluating stably expressed genes in single cells.
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- GigaScience, 2019, v. 8, n. 9, p. N.PAG, doi. 10.1093/gigascience/giz106
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Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data.
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- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02622-0
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- Article
Feature selection revisited in the single-cell era.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02544-3
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- Article
KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis.
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- Proteomics, 2016, v. 16, n. 13, p. 1868, doi. 10.1002/pmic.201600068
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- Article
Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis.
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- eLife, 2021, p. 1, doi. 10.7554/eLife.66942
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- Article
Global redox proteome and phosphoproteome analysis reveals redox switch in Akt.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-13114-4
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- Article
NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10905-7
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- Article
Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments.
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- Cytometry. Part A, 2023, v. 103, n. 7, p. 593, doi. 10.1002/cyto.a.24729
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- Article
Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal.
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- EMBO Journal, 2014, v. 33, n. 8, p. 878, doi. 10.1002/embj.201386537
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- Article
Gene-gene interaction filtering with ensemble of filters.
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- BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S10
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- Article
A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data.
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- BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-S1-S5
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- Article
A genetic ensemble approach for gene-gene interaction identification.
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- BMC Bioinformatics, 2010, v. 11, p. 524, doi. 10.1186/1471-2105-11-524
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- Article
Vascular senescence and leak are features of the early breakdown of the blood–brain barrier in Alzheimer's disease models.
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- GeroScience, 2023, v. 45, n. 6, p. 3307, doi. 10.1007/s11357-023-00927-x
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- Article
Single‐Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression.
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- Advanced Science, 2022, v. 9, n. 3, p. 1, doi. 10.1002/advs.202103631
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- Article
Single‐Cell Transcriptome Profiling Reveals Multicellular Ecosystem of Nucleus Pulposus during Degeneration Progression (Adv. Sci. 3/2022).
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- Advanced Science, 2022, v. 9, n. 3, p. 1, doi. 10.1002/advs.202270016
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- Article
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis.
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- BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-3179-5
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- Article
scDC: single cell differential composition analysis.
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- BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-3211-9
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- Article
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference.
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- Molecular Systems Biology, 2020, v. 16, n. 6, p. 1, doi. 10.15252/msb.20199389
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- Article
Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.
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- PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004403
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- Article
Computational systems approach towards phosphoproteomics and their downstream regulation.
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- Proteomics, 2023, v. 23, n. 3/4, p. 1, doi. 10.1002/pmic.202200068
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- Article
QCMAP: An Interactive Web‐Tool for Performance Diagnosis and Prediction of LC‐MS Systems.
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- Proteomics, 2019, v. 19, n. 13, p. 1, doi. 10.1002/pmic.201900068
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- Article
Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 3, p. 1, doi. 10.1093/bib/bbad159
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- Article
Impact of similarity metrics on single-cell RNA-seq data clustering.
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- Briefings in Bioinformatics, 2019, v. 20, n. 6, p. 2316, doi. 10.1093/bib/bby076
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- Article
DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis.
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- Nature Communications, 2015, v. 6, n. 4, p. 6910, doi. 10.1038/ncomms7910
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- Article
Evaluating spatially variable gene detection methods for spatial transcriptomics data.
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- Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-023-03145-y
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- Publication type:
- Article
Evaluation of deep learning-based feature selection for single-cell RNA sequencing data analysis.
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- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03100-x
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- Article
Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies.
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- PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157763
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- Article
Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells.
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- Cell Death Discovery, 2021, v. 7, n. 1, p. 1, doi. 10.1038/s41420-021-00456-6
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- Article
Multi-task learning from multimodal single-cell omics with Matilda.
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- Nucleic Acids Research, 2023, v. 51, n. 8, p. e45, doi. 10.1093/nar/gkad157
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- Article
Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning.
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- Nucleic Acids Research, 2020, v. 48, n. 4, p. 1828, doi. 10.1093/nar/gkz1179
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- Article
The impact of similarity metrics on cell-type clustering in highly multiplexed in situ imaging cytometry data.
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- Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad141
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- Article
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era.
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- Briefings in Functional Genomics, 2022, v. 21, n. 4, p. 270, doi. 10.1093/bfgp/elac008
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- Article
Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles.
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- BMC Genomics, 2010, v. 11, p. 1, doi. 10.1186/1471-2164-11-S4-S22
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- Article
A particle swarm based hybrid system for imbalanced medical data sampling.
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- BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-S3-S34
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- Article
CiteFuse enables multi-modal analysis of CITE-seq data.
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- Bioinformatics, 2020, v. 36, n. 14, p. 4137, doi. 10.1093/bioinformatics/btaa282
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- Article
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.
- Published in:
- Bioinformatics, 2017, v. 33, n. 13, p. 1916, doi. 10.1093/bioinformatics/btx092
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- Article
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data.
- Published in:
- Bioinformatics, 2016, v. 32, n. 2, p. 252, doi. 10.1093/bioinformatics/btv550
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- Publication type:
- Article
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway.
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- Bioinformatics, 2014, v. 30, n. 6, p. 808, doi. 10.1093/bioinformatics/btt616
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- Article