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Representing mutations for predicting cancer drug response.
- Published in:
- Bioinformatics, 2024, v. 40, p. i160, doi. 10.1093/bioinformatics/btae209
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- Publication type:
- Article
In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells.
- Published in:
- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-63943-7
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- Publication type:
- Article
Mapping the common gene networks that underlie related diseases.
- Published in:
- Nature Protocols, 2023, v. 18, n. 6, p. 1745, doi. 10.1038/s41596-022-00797-1
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- Publication type:
- Article
Hierarchical association of COPD to principal genetic components of biological systems.
- Published in:
- PLoS ONE, 2023, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0286064
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- Publication type:
- Article
Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation.
- Published in:
- Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-33329-2
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- Publication type:
- Article
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
- Published in:
- Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad118
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- Publication type:
- Article
Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging.
- Published in:
- Journal of Internal Medicine, 2022, v. 292, n. 5, p. 733, doi. 10.1111/joim.13533
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- Publication type:
- Article
An open invitation to the Understudied Proteins Initiative.
- Published in:
- 2022
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- Publication type:
- Letter
Deep distributed computing to reconstruct extremely large lineage trees.
- Published in:
- Nature Biotechnology, 2022, v. 40, n. 4, p. 566, doi. 10.1038/s41587-021-01111-2
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- Publication type:
- Article
Genetic dissection of complex traits using hierarchical biological knowledge.
- Published in:
- PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1009373
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- Publication type:
- Article
Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging.
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- Cerebral Cortex, 2021, v. 31, n. 8, p. 3752, doi. 10.1093/cercor/bhab045
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- Publication type:
- Article
HiDeF: identifying persistent structures in multiscale 'omics data.
- Published in:
- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02228-4
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- Publication type:
- Article
Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.
- Published in:
- 2021
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- Publication type:
- Correction Notice
Multiscale community detection in Cytoscape.
- Published in:
- PLoS Computational Biology, 2020, v. 16, n. 10, p. 1, doi. 10.1371/journal.pcbi.1008239
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- Publication type:
- Article
Association of Epigenetic Metrics of Biological Age With Cortical Thickness.
- Published in:
- JAMA Network Open, 2020, v. 3, n. 9, p. e2015428, doi. 10.1001/jamanetworkopen.2020.15428
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- Publication type:
- Article
Genome-wide dynamic evaluation of the UV-induced DNA damage response.
- Published in:
- G3: Genes | Genomes | Genetics, 2020, v. 10, n. 9, p. 1, doi. 10.1534/g3.120.401417
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- Publication type:
- Article
Thousands of missing variants in the UK Biobank are recoverable by genome realignment.
- Published in:
- Annals of Human Genetics, 2020, v. 84, n. 3, p. 214, doi. 10.1111/ahg.12383
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- Publication type:
- Article
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14500-z
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- Publication type:
- Article
Dynamic post-translational modification profiling of Mycobacterium tuberculosisinfected primary macrophages.
- Published in:
- eLife, 2020, p. 1, doi. 10.7554/eLife.51461
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- Publication type:
- Article
The great hairball gambit.
- Published in:
- PLoS Genetics, 2019, v. 15, n. 11, p. 1, doi. 10.1371/journal.pgen.1008519
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- Publication type:
- Article
DNA methylation aging clocks: challenges and recommendations.
- Published in:
- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1824-y
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- Publication type:
- Article
Classifying tumors by supervised network propagation.
- Published in:
- Bioinformatics, 2019, v. 35, n. 14, p. 2528, doi. 10.1093/bioinformatics/bty1072
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- Publication type:
- Article
Rare variant phasing using paired tumor:normal sequence data.
- Published in:
- BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2753-1
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- Publication type:
- Article
A Blueprint for Systems Biology.
- Published in:
- Clinical Chemistry, 2019, v. 65, n. 2, p. 342, doi. 10.1373/clinchem.2018.291062
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- Publication type:
- Article
Typing tumors using pathways selected by somatic evolution.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06464-y
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- Publication type:
- Article
Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas.
- Published in:
- Genome Medicine, 2018, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13073-018-0579-5
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- Publication type:
- Article
Classifying tumors by supervised network propagation.
- Published in:
- Bioinformatics, 2018, v. 34, n. 13, p. i484, doi. 10.1093/bioinformatics/bty247
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- Publication type:
- Article
ndexr--an R package to interface with the network data exchange.
- Published in:
- Bioinformatics, 2018, v. 34, n. 4, p. 716, doi. 10.1093/bioinformatics/btx683
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- Publication type:
- Article
Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia.
- Published in:
- Nature Communications, 2017, v. 8, n. 11, p. 1, doi. 10.1038/s41467-017-01439-x
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- Publication type:
- Article
Network propagation in the cytoscape cyberinfrastructure.
- Published in:
- PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005598
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- Publication type:
- Article
Network approaches and applications in biology.
- Published in:
- PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005771
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- Publication type:
- Article
Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.
- Published in:
- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3770-y
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- Publication type:
- Article
Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1185-3
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- Publication type:
- Article
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1186-2
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- Publication type:
- Article
Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.
- Published in:
- International Journal of Cancer, 2016, v. 139, n. 2, p. 373, doi. 10.1002/ijc.30081
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- Publication type:
- Article
Challenges in identifying cancer genes by analysis of exome sequencing data.
- Published in:
- Nature Communications, 2016, v. 7, n. 7, p. 12096, doi. 10.1038/ncomms12096
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- Publication type:
- Article
Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy.
- Published in:
- Journal of Endourology, 2016, v. 30, n. 1, p. 114, doi. 10.1089/end.2015.0411
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- Publication type:
- Article
Evidence for a common evolutionary rate in metazoan transcriptional networks.
- Published in:
- eLife, 2015, p. 1, doi. 10.7554/eLife.11615
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- Publication type:
- Article
Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types.
- Published in:
- PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0142618
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- Publication type:
- Article
Molecular networks in context.
- Published in:
- Nature Biotechnology, 2015, v. 33, n. 7, p. 720, doi. 10.1038/nbt.3283
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- Publication type:
- Article
ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer.
- Published in:
- PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0126898
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- Publication type:
- Article
Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress.
- Published in:
- Environmental Health Perspectives, 2014, v. 122, n. 12, p. 1271, doi. 10.1289/ehp.1408418
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- Publication type:
- Article
Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice.
- Published in:
- 2014
- By:
- Publication type:
- journal article
Matrix-Metalloproteinases in Head and Neck Carcinoma–Cancer Genome Atlas Analysis and Fluorescence Imaging in Mice.
- Published in:
- Otolaryngology-Head & Neck Surgery, 2014, v. 151, n. 4, p. 612, doi. 10.1177/0194599814545083
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- Publication type:
- Article
Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss.
- Published in:
- Nature Genetics, 2014, v. 46, n. 9, p. 939, doi. 10.1038/ng.3051
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- Publication type:
- Article
Inferring gene ontologies from pairwise similarity data.
- Published in:
- Bioinformatics, 2014, v. 30, n. 12, p. i34, doi. 10.1093/bioinformatics/btu282
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- Publication type:
- Article
An Integrated Map of HIV-Human Protein Complexes that Facilitate Viral Infection.
- Published in:
- PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0096687
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- Publication type:
- Article
Rac2 Controls Tumor Growth, Metastasis and M1-M2 Macrophage Differentiation <i>In Vivo</i>.
- Published in:
- PLoS ONE, 2014, v. 9, n. 4, p. 1, doi. 10.1371/journal.pone.0095893
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- Publication type:
- Article
NeXO Web: the NeXO ontology database and visualization platform.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. D1, p. D1269, doi. 10.1093/nar/gkt1192
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- Publication type:
- Article
Development of Ultra-High-Density Screening Tools for Microbial “Omics”.
- Published in:
- PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0085177
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- Publication type:
- Article