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Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data

Genome Biology, 2022-02, Vol.23 (1), p.49-21, Article 49

2022

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scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

Nature biotechnology, 2022-05, Vol.40 (5), p.703-710

2022

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Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition

Nature communications, 2020-04, Vol.11 (1), p.1897-1897, Article 1897

2020

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Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

BMC bioinformatics, 2019-12, Vol.20 (Suppl 19), p.660-11, Article 660

2019

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3D reconstruction of spatial expression

Nature methods, 2022-05, Vol.19 (5), p.526-527

2022

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Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

Nature communications, 2023-07, Vol.14 (1), p.4272-4272, Article 4272

2023

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Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

Cell metabolism, 2013-06, Vol.17 (6), p.1009-1020

2013

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Scalable workflow for characterization of cell-cell communication in COVID-19 patients

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010495

2022

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BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

Nature communications, 2024-01, Vol.15 (1), p.509-509, Article 509

2024

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The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease

Journal of neurology, 2022-02, Vol.269 (2), p.780-795

2022

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Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development

BMC genomics, 2017-12, Vol.18 (1), p.946-946, Article 946

2017

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PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors

Clinical cancer research, 2017-10, Vol.23 (20), p.6054-6061

2017

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scDC: single cell differential composition analysis

BMC bioinformatics, 2019-12, Vol.20 (Suppl 19), p.721-721, Article 721

2019

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LC-N2G: a local consistency approach for nutrigenomics data analysis

BMC bioinformatics, 2020-11, Vol.21 (1), p.530-530, Article 530

2020

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Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF -Mutant Melanoma

Clinical cancer research, 2019-02, Vol.25 (4), p.1272-1279

2019

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Imputation of plasma lipid species to facilitate integration of lipidomic datasets

Nature communications, 2024-02, Vol.15 (1), p.1540-1540, Article 1540

2024

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Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma

Cancers, 2022-10, Vol.14 (21), p.5213

2022

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Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis

PloS one, 2017-06, Vol.12 (6), p.e0180378-e0180378

2017

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Integrated single cell data analysis reveals cell specific networks and novel coactivation markers

BMC systems biology, 2016-12, Vol.10 (Suppl 5), p.127-127, Article 127

2016

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Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes

Oncotarget, 2015-09, Vol.6 (29), p.27023-27036

2015

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Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods

Journal of proteome research, 2017-07, Vol.16 (7), p.2359-2369

2017

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Evaluating stably expressed genes in single cells

Gigascience, 2019-09, Vol.8 (9)

2019

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Lipidomics Profiling and Risk of Coronary Artery Disease in the BioHEART-CT Discovery Cohort

Biomolecules (Basel, Switzerland), 2023-05, Vol.13 (6), p.917

2023

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The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies

Frontiers in aging neuroscience, 2022-05, Vol.14, p.875261

2022

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Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1-Based Immunotherapy

Clinical cancer research, 2019-03, Vol.25 (5), p.1557-1563

2019

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Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning

Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition

Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis

3D reconstruction of spatial expression

Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

Scalable workflow for characterization of cell-cell communication in COVID-19 patients

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

The impact of device-assisted therapies on the gut microbiome in Parkinson’s disease

Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development

PD-L1 Expression and Immune Escape in Melanoma Resistance to MAPK Inhibitors

scDC: single cell differential composition analysis

LC-N2G: a local consistency approach for nutrigenomics data analysis

Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF -Mutant Melanoma

Imputation of plasma lipid species to facilitate integration of lipidomic datasets

Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma

Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis

Integrated single cell data analysis reveals cell specific networks and novel coactivation markers

Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes

Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods

Evaluating stably expressed genes in single cells

Lipidomics Profiling and Risk of Coronary Artery Disease in the BioHEART-CT Discovery Cohort

The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies

Circulating Cytokines Predict Immune-Related Toxicity in Melanoma Patients Receiving Anti-PD-1-Based Immunotherapy

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