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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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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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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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Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data

Briefings in bioinformatics, 2022-09, Vol.23 (5)

2022

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VarSCAT: A computational tool for sequence context annotations of genomic variants

PLoS computational biology, 2023-08, Vol.19 (8), p.e1010727-e1010727

2023

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Comparison of software packages for detecting differential expression in RNA-seq studies

Briefings in bioinformatics, 2015-01, Vol.16 (1), p.59-70

2015

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Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009269-e1009269

2022

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A survey of best practices for RNA-seq data analysis

Genome Biology, 2016-01, Vol.17 (1), p.13-13, Article 13

2016

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Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases

The Journal of clinical investigation, 2020-01, Vol.130 (1), p.20-28

2020

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Systematic evaluation of differential splicing tools for RNA-seq studies

Briefings in bioinformatics, 2020-12, Vol.21 (6), p.2052-2065

2020

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Development of prediction model for alanine transaminase elevations during the first 6 months of conventional synthetic DMARD treatment

Scientific reports, 2023-08, Vol.13 (1), p.12943-12943, Article 12943

2023

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Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial

Gut, 2021-02, p.gutjnl-2020-321643

2021

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Polymorphism in interferon alpha/beta receptor contributes to glucocorticoid response and outcome of ARDS and COVID-19

Critical care (London, England), 2023-03, Vol.27 (1), p.112-112, Article 112

2023

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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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Comparison of methods to detect differentially expressed genes between single-cell populations

Briefings in bioinformatics, 2017-09, Vol.18 (5), p.735-743

2017

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A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation

Nucleic acids research, 2022-05, Vol.50 (9), p.4938-4958

2022

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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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A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments

PloS one, 2014-12, Vol.9 (12), p.e115964-e115964

2014

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Deep Learning Enables Automatic Detection of Joint Damage Progression in Rheumatoid Arthritis-Model Development and External Validation

Rheumatology (Oxford, England), 2024-04

2024

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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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Gut microbiota composition is associated with temperament traits in infants

Brain, behavior, and immunity, 2019-08, Vol.80, p.849-858

2019

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Stable Iterative Variable Selection

Bioinformatics, 2021-12, Vol.37 (24), p.4810-4817

2021

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A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

BMC genomics, 2009-12, Vol.10 (1), p.618-618, Article 618

2009

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Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies

RNA biology, 2021-11, Vol.18 (11), p.1739-1746

2021

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scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data

Bioinformatics (Oxford, England), 2022-02, Vol.38 (5), p.1328-1335

2022

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

ROTS: An R package for reproducibility-optimized statistical testing

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

Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data

VarSCAT: A computational tool for sequence context annotations of genomic variants

Comparison of software packages for detecting differential expression in RNA-seq studies

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

A survey of best practices for RNA-seq data analysis

Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases

Systematic evaluation of differential splicing tools for RNA-seq studies

Development of prediction model for alanine transaminase elevations during the first 6 months of conventional synthetic DMARD treatment

Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial

Polymorphism in interferon alpha/beta receptor contributes to glucocorticoid response and outcome of ARDS and COVID-19

Enhanced differential expression statistics for data-independent acquisition proteomics

Comparison of methods to detect differentially expressed genes between single-cell populations

A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation

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

A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments

Deep Learning Enables Automatic Detection of Joint Damage Progression in Rheumatoid Arthritis-Model Development and External Validation

Computational solutions for spatial transcriptomics

Gut microbiota composition is associated with temperament traits in infants

Stable Iterative Variable Selection

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies

scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data

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