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Enhanced differential expression statistics for data-independent acquisition proteomics

Scientific reports, 2017-07, Vol.7 (1), p.5869-8, Article 5869

2017

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ROTS: An R package for reproducibility-optimized statistical testing

PLoS computational biology, 2017-05, Vol.13 (5), p.e1005562-e1005562

2017

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Computational solutions for spatial transcriptomics

Computational and structural biotechnology journal, 2022-01, Vol.20, p.4870-4884

2022

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Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory

Diabetologia, 2023-11, Vol.66 (11), p.1983-1996

2023

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Distinct cellular immune responses in children en route to type 1 diabetes with different first-appearing autoantibodies

Nature communications, 2024-05, Vol.15 (1), p.3810-3810, Article 3810

2024

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Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach

Nature communications, 2022-12, Vol.13 (1), p.7877-18, Article 7877

2022

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Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer

Nature communications, 2021-11, Vol.12 (1), p.6967-6967, Article 6967

2021

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COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts

Frontiers in genetics, 2022-08, Vol.13, p.929887

2022

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SimPhospho: a software tool enabling confident phosphosite assignment

Bioinformatics, 2018-08, Vol.34 (15), p.2690-2692

2018

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Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk

iScience, 2024-06, Vol.27 (6), p.110048-110048, Article 110048

2024

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Improved risk prediction of chemotherapy‐induced neutropenia—model development and validation with real‐world data

Cancer medicine (Malden, MA), 2022-02, Vol.11 (3), p.654-663

2022

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A systematic evaluation of normalization methods in quantitative label-free proteomics

Briefings in bioinformatics, 2018-01, Vol.19 (1), p.1-11

2018

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HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma

Cancer & metabolism, 2017-07, Vol.5 (1), p.5-17, Article 5

2017

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A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation

Briefings in bioinformatics, 2018-11, Vol.19 (6), p.1344-1355

2018

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Statistical and machine learning methods to study human CD4+ T cell proteome profiles

Immunology letters, 2022-05, Vol.245, p.8-17

2022

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Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential

Cellular and molecular life sciences : CMLS, 2024-12, Vol.81 (1), p.399, Article 399

2024

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Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut MicrobiotaImplementation and Computational Analysis

Journal of proteome research, 2020-01, Vol.19 (1), p.432-436

2020

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Correction to: PhosPiR: an automated phosphoproteomic pipeline in R

Briefings in bioinformatics, 2022-05, Vol.23 (3)

2022

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Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins

Journal of proteome research, 2015-11, Vol.14 (11), p.4564-4570

2015

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Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics

Bioinformatics, 2018-02, Vol.34 (4), p.693-694

2018

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ECCB2024: The 23rd European Conference on Computational Biology

Bioinformatics (Oxford, England), 2024-09, Vol.40 (Supplement_2), p.ii1-ii3

2024

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Disruption of HSD17B12 in mouse hepatocytes leads to reduced body weight and defect in the lipid droplet expansion associated with microvesicular steatosis

The FASEB journal, 2024-09, Vol.38 (17), p.e70034-n/a

2024

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PhosPiR: an automated phosphoproteomic pipeline in R

Briefings in bioinformatics, 2022-01, Vol.23 (1)

2022

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Accurate Detection of Differential Expression and Splicing Using Low-Level Features

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1507, p.141

2017

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Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples

ISME Communications, 2022-06, Vol.2 (1)

2022

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Enhanced differential expression statistics for data-independent acquisition proteomics

ROTS: An R package for reproducibility-optimized statistical testing

Computational solutions for spatial transcriptomics

Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory

Distinct cellular immune responses in children en route to type 1 diabetes with different first-appearing autoantibodies

Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach

Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer

COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts

SimPhospho: a software tool enabling confident phosphosite assignment

Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes risk

Improved risk prediction of chemotherapy‐induced neutropenia—model development and validation with real‐world data

A systematic evaluation of normalization methods in quantitative label-free proteomics

HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma

A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation

Statistical and machine learning methods to study human CD4+ T cell proteome profiles

Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential

Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut MicrobiotaImplementation and Computational Analysis

Correction to: PhosPiR: an automated phosphoproteomic pipeline in R

Using Peptide-Level Proteomics Data for Detecting Differentially Expressed Proteins

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics

ECCB2024: The 23rd European Conference on Computational Biology

Disruption of HSD17B12 in mouse hepatocytes leads to reduced body weight and defect in the lipid droplet expansion associated with microvesicular steatosis

PhosPiR: an automated phosphoproteomic pipeline in R

Accurate Detection of Differential Expression and Splicing Using Low-Level Features

Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples

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