Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics

Fibroblast-Specific Proteo-Transcriptomes Reveal Distinct Fibrotic Signatures of Human Sinoatrial Node in Non-Failing and Failing Hearts

(2021) Anuradha Kalyanasundaram et al.   CIRCULATION

Comparative evaluation of label-free quantification strategies

(2020) Lei Zhao et al.   Journal of Proteomics

Tagging enhances histochemical and biochemical detection of Ran Binding Protein 9 in vivo and reveals its interaction with Nucleolin

(2020) Shimaa H. A. Soliman et al.   Scientific Reports

Proper imputation of missing values in proteomics datasets for differential expression analysis

(2020) Mingyi Liu et al.   BRIEFINGS IN BIOINFORMATICS

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data

(2020) Laurent Gatto et al.   JOURNAL OF PROTEOME RESEARCH

A microfluidic chip enables isolation of exosomes and establishment of their protein profiles and associated signaling pathways in ovarian cancer

(2019) Kalpana Deepa Priya Dorayappan et al.   CANCER RESEARCH

GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis

(2019) Qian Li et al.   BIOINFORMATICS

Advances in Current Diabetes Proteomics: From the Perspectives of Label-free Quantification and Biomarker Selection

(2019) Jianbo Fu et al.   CURRENT DRUG TARGETS

The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia

(2019) Dimitrios Papaioannou et al.   Nature Communications

Refinements of LC-MS/MS Spectral Counting Statistics Improve Quantification of Low Abundance Proteins

(2019) Ha Yun Lee et al.   Scientific Reports

PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data

(2018) Cheng Chang et al.   BIOINFORMATICS

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

(2018) Runmin Wei et al.   PLoS Computational Biology

statTarget: A streamlined tool for signal drift correction and interpretations of quantitative mass spectrometry-based omics data

(2018) Hemi Luan et al.   ANALYTICA CHIMICA ACTA

Learning and Imputation for Mass-spec Bias Reduction (LIMBR)

(2018) Alexander M Crowell et al.   BIOINFORMATICS

Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data

(2018) Runmin Wei et al.   Scientific Reports

The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments

(2018) Jonathon J. O’Brien et al.   Annals of Applied Statistics

Integrated identification and quantification error probabilities for shotgun proteomics

(2018) Matthew The et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

(2017) Kuan-lin Huang et al.   Nature Communications

In-depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values

(2017) Jinxia Wang et al.   Scientific Reports

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics

(2016) Samuel Wieczorek et al.   BIOINFORMATICS

Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework

(2016) Valentin Voillet et al.   BMC BIOINFORMATICS

Tag-Count Analysis of Large-Scale Proteomic Data

(2016) Owen E. Branson et al.   JOURNAL OF PROTEOME RESEARCH

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies

(2016) Cosmin Lazar et al.   JOURNAL OF PROTEOME RESEARCH

A multi-model statistical approach for proteomic spectral count quantitation

(2016) Owen E. Branson et al.   Journal of Proteomics

Dynamic Protein Interactions of the Polycomb Repressive Complex 2 during Differentiation of Pluripotent Cells

(2016) Giorgio Oliviero et al.   MOLECULAR & CELLULAR PROTEOMICS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

(2015) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

Multiple imputation and analysis for high-dimensional incomplete proteomics data

(2015) Xiaoyan Yin et al.   STATISTICS IN MEDICINE

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

(2014) Richard Alexander Scheltema et al.   MOLECULAR & CELLULAR PROTEOMICS

Normalization and missing value imputation for label-free LC-MS analysis

(2012) Yuliya V Karpievitch et al.   BMC BIOINFORMATICS

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

(2011) Laurent Gatto et al.   BIOINFORMATICS

Discovery of Mouse Spleen Signaling Responses to Anthrax using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry

(2010) Nathan P. Manes et al.   MOLECULAR & CELLULAR PROTEOMICS

A statistical framework for protein quantitation in bottom-up MS-based proteomics

(2009) Yuliya Karpievitch et al.   BIOINFORMATICS

Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition

(2009) Yuliya V. Karpievitch et al.   BIOINFORMATICS