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Integrative analysis of genomic and epigenomic regulation reveals miRNA mediated tumor heterogeneity and immune evasion in lower grade glioma.
- Published in:
- Communications Biology, 2024, v. 7, n. 7, p. 1, doi. 10.1038/s42003-024-06488-9
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- Publication type:
- Article
Computational single-cell methods for predicting cancer risk.
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- Biochemical Society Transactions, 2024, v. 52, n. 3, p. 1503, doi. 10.1042/BST20231488
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- Article
Longitudinal analysis of epigenome-wide DNA methylation reveals novel loci associated with BMI change in East Asians.
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- Clinical Epigenetics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13148-024-01679-x
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- Article
An improved epigenetic counter to track mitotic age in normal and precancerous tissues.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48649-8
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- Article
A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes.
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- Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01211-5
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- Publication type:
- Article
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39017-z
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- Publication type:
- Article
Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies.
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- Clinical Epigenetics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13148-022-01253-3
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- Article
Novel epigenetic network biomarkers for early detection of esophageal cancer.
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- Clinical Epigenetics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13148-022-01243-5
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- Article
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data.
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- Bioinformatics, 2021, v. 37, n. 11, p. 1528, doi. 10.1093/bioinformatics/btaa987
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- Article
Improved detection of tumor suppressor events in single-cell RNA-Seq data.
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- NPJ Genomic Medicine, 2020, v. 5, n. 1, p. N.PAG, doi. 10.1038/s41525-020-00151-y
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- Publication type:
- Article
A cell-type deconvolution meta-analysis of whole blood EWAS reveals lineage-specific smoking-associated DNA methylation changes.
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- Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-18618-y
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- Publication type:
- Article
EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data.
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- Genome Biology, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s13059-020-02126-9
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- Article
A comparison of epigenetic mitotic-like clocks for cancer risk prediction.
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- Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-00752-3
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- Publication type:
- Article
EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI.
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- Bioinformatics, 2020, v. 36, n. 6, p. 1950, doi. 10.1093/bioinformatics/btz833
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- Article
Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures.
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- Briefings in Bioinformatics, 2020, v. 21, n. 1, p. 248, doi. 10.1093/bib/bby093
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- Article
DNA methylation aging clocks: challenges and recommendations.
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- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1824-y
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- Publication type:
- Article
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.
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- Bioinformatics, 2019, v. 35, n. 22, p. 4767, doi. 10.1093/bioinformatics/btz456
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- Article
Appraising the causal relevance of DNA methylation for risk of lung cancer.
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- 2019
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- Publication type:
- journal article
ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies.
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- Bioinformatics, 2019, v. 35, n. 18, p. 3514, doi. 10.1093/bioinformatics/btz073
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- Publication type:
- Article
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.
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- Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0554-8
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- Publication type:
- Article
Detection of epigenetic field defects using a weighted epigenetic distance-based method.
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- Nucleic Acids Research, 2019, v. 47, n. 1, p. e6, doi. 10.1093/nar/gky882
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- Publication type:
- Article
Accounting for differential variability in detecting differentially methylated regions.
- Published in:
- Briefings in Bioinformatics, 2019, v. 20, n. 1, p. 47, doi. 10.1093/bib/bbx097
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- Publication type:
- Article
Tensorial blind source separation for improved analysis of multi-omic data.
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- Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1455-8
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- Publication type:
- Article
Psychosocial adversity and socioeconomic position during childhood and epigenetic age: analysis of two prospective cohort studies.
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- Human Molecular Genetics, 2018, v. 27, n. 7, p. 1301, doi. 10.1093/hmg/ddy036
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- Publication type:
- Article
Roadmap for investigating epigenome deregulation and environmental origins of cancer.
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- International Journal of Cancer, 2018, v. 142, n. 5, p. 874, doi. 10.1002/ijc.31014
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- Publication type:
- Article
Tumor origin detection with tissue-specific miRNA and DNA methylation markers.
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- Bioinformatics, 2018, v. 34, n. 3, p. 398, doi. 10.1093/bioinformatics/btx622
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- Publication type:
- Article
The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer.
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- Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0500-7
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- Publication type:
- Article
Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development.
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- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1366-0
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- Publication type:
- Article
ChAMP: updated methylation analysis pipeline for Illumina BeadChips.
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- Bioinformatics, 2017, v. 33, n. 24, p. 3982, doi. 10.1093/bioinformatics/btx513
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- Publication type:
- Article
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome.
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- Nature Communications, 2017, v. 8, n. 6, p. 15599, doi. 10.1038/ncomms15599
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- Publication type:
- Article
DNA methylome analysis reveals distinct epigenetic patterns of ascending aortic dissection and bicuspid aortic valve.
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- Cardiovascular Research, 2017, v. 113, n. 6, p. 692, doi. 10.1093/cvr/cvx050
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- Publication type:
- Article
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
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- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1511-5
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- Publication type:
- Article
Epigenetic and genetic deregulation in cancer target distinct signaling pathway domains.
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- Nucleic Acids Research, 2017, v. 45, n. 2, p. 583, doi. 10.1093/nar/gkw1100
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- Publication type:
- Article
dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers.
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- Nucleic Acids Research, 2017, v. 45, n. D1, p. D812, doi. 10.1093/nar/gkw1079
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- Publication type:
- Article
The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation.
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- Nucleic Acids Research, 2016, v. 44, n. 22, p. 10631, doi. 10.1093/nar/gkw802
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- Publication type:
- Article
Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.
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- Nature Communications, 2016, v. 7, n. 11, p. 13555, doi. 10.1038/ncomms13555
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- Publication type:
- Article
Correlation of an epigenetic mitotic clock with cancer risk.
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- Genome Biology, 2016, v. 17, p. 1, doi. 10.1186/s13059-016-1064-3
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- Publication type:
- Article
The multi-omic landscape of transcription factor inactivation in cancer.
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- Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0342-8
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- Publication type:
- Article
Stochastic epigenetic outliers can define field defects in cancer.
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- BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1056-z
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- Publication type:
- Article
Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer.
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- Epigenetics & Chromatin, 2016, v. 9, p. 1, doi. 10.1186/s13072-016-0058-4
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- Publication type:
- Article
DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.
- Published in:
- Nature Communications, 2016, v. 7, n. 1, p. 10478, doi. 10.1038/ncomms10478
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- Publication type:
- Article
The integrative epigenomic-transcriptomic landscape of ER positive breast cancer.
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- Clinical Epigenetics, 2015, v. 7, p. 1, doi. 10.1186/s13148-015-0159-0
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- Publication type:
- Article
Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer.
- Published in:
- Genome Biology, 2015, v. 16, n. 1, p. 61, doi. 10.1186/s13059-015-0630-4
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- Publication type:
- Article
An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer
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- Genome Biology, 2015, v. 16, n. 1, p. 140, doi. 10.1186/s13059-015-0699-9
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- Publication type:
- Article
Increased signaling entropy in cancer requires the scale-free property of protein interaction networks.
- Published in:
- Scientific Reports, 2015, p. 9646, doi. 10.1038/srep09646
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- Publication type:
- Article
Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer.
- Published in:
- PLoS Computational Biology, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004115
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- Publication type:
- Article
An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging.
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- PLoS Genetics, 2015, v. 11, n. 2, p. 1, doi. 10.1371/journal.pgen.1004996
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- Publication type:
- Article
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control.
- Published in:
- Bioinformatics, 2014, v. 30, n. 16, p. 2360, doi. 10.1093/bioinformatics/btu316
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- Publication type:
- Article
A BRCA1-mutation associated DNA methylation signature in blood cells predicts sporadic breast cancer incidence and survival.
- Published in:
- Genome Medicine, 2014, v. 6, n. 6, p. 1, doi. 10.1186/gm567
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- Publication type:
- Article
The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis.
- Published in:
- PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003709
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- Article