Reuse of public genome-wide gene expression data

J Rung, A Brazma - Nature Reviews Genetics, 2013 - nature.com
Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

Comprehensive literature review and statistical considerations for microarray meta-analysis

GC Tseng, D Ghosh, E Feingold - Nucleic acids research, 2012 - academic.oup.com
With the rapid advances of various high-throughput technologies, generation of '-omics' data
is commonplace in almost every biomedical field. Effective data management and analytical …

Evaluation of a decided sample size in machine learning applications

D Rajput, WJ Wang, CC Chen - BMC bioinformatics, 2023 - Springer
Background An appropriate sample size is essential for obtaining a precise and reliable
outcome of a study. In machine learning (ML), studies with inadequate samples suffer from …

Pan-cancer single-cell landscape of tumor-infiltrating T cells

L Zheng, S Qin, W Si, A Wang, B **ng, R Gao, X Ren… - Science, 2021 - science.org
INTRODUCTION Cancer immunotherapies that target tumor-specific T cells have benefited
many cancer patients, but the clinical efficacy varies greatly among different cancer types …

[HTML][HTML] Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation

Y Gao, J Li, W Cheng, T Diao, H Liu, Y Bo, C Liu… - Cancer Cell, 2024 - cell.com
Fibroblasts, known for their functional diversity, play crucial roles in inflammation and
cancer. In this study, we conduct comprehensive single-cell RNA sequencing analyses on …

Ranking treatments in frequentist network meta-analysis works without resampling methods

G Rücker, G Schwarzer - BMC medical research methodology, 2015 - Springer
Background Network meta-analysis is used to compare three or more treatments for the
same condition. Within a Bayesian framework, for each treatment the probability of being …

Integrating pathways of Parkinson's disease in a molecular interaction map

KA Fujita, M Ostaszewski, Y Matsuoka, S Ghosh… - Molecular …, 2014 - Springer
Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused
by a complex interplay of genetic and environmental factors. Information on various aspects …

A survey of gene expression meta-analysis: methods and applications

D Toro-Domínguez, JA Villatoro-Garciá… - Briefings in …, 2021 - academic.oup.com
The increasing use of high-throughput gene expression quantification technologies over the
last two decades and the fact that most of the published studies are stored in public …

INMEX—a web-based tool for integrative meta-analysis of expression data

J **a, CD Fjell, ML Mayer, OM Pena… - Nucleic acids …, 2013 - academic.oup.com
The widespread applications of various 'omics' technologies in biomedical research together
with the emergence of public data repositories have resulted in a plethora of data sets for …

Differential meta-analysis of RNA-seq data from multiple studies

A Rau, G Marot, F Jaffrézic - BMC bioinformatics, 2014 - Springer
Background High-throughput sequencing is now regularly used for studies of the
transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For …