A survey of best practices for RNA-seq data analysis
Abstract RNA-sequencing (RNA-seq) has a wide variety of applications, but no single
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data …
–Omic and electronic health record big data analytics for precision medicine
PY Wu, CW Cheng, CD Kaddi… - IEEE Transactions …, 2016 - ieeexplore.ieee.org
Objective: Rapid advances of high-throughput technologies and wide adoption of electronic
health records (EHRs) have led to fast accumulation of–omic and EHR data. These …
health records (EHRs) have led to fast accumulation of–omic and EHR data. These …
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Despite the many approaches to study differential splicing from RNA-seq, many challenges
remain unsolved, including computing capacity and sequencing depth requirements. Here …
remain unsolved, including computing capacity and sequencing depth requirements. Here …
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability
M Munschauer, CT Nguyen, K Sirokman, CR Hartigan… - Nature, 2018 - nature.com
The human genome contains thousands of long non-coding RNAs, but specific biological
functions and biochemical mechanisms have been discovered for only about a dozen,,,,–. A …
functions and biochemical mechanisms have been discovered for only about a dozen,,,,–. A …
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide
analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of …
analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of …
A new view of transcriptome complexity and regulation through the lens of local splicing variations
J Vaquero-Garcia, A Barrera, MR Gazzara… - elife, 2016 - elifesciences.org
Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing
variations remains a challenge. Here, we propose a new approach to define and quantify …
variations remains a challenge. Here, we propose a new approach to define and quantify …
Systematic evaluation of differential splicing tools for RNA-seq studies
A Mehmood, A Laiho, MS Venäläinen… - Briefings in …, 2020 - academic.oup.com
Differential splicing (DS) is a post-transcriptional biological process with critical, wide-
ranging effects on a plethora of cellular activities and disease processes. To date, a number …
ranging effects on a plethora of cellular activities and disease processes. To date, a number …
Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes
Head and neck squamous cell carcinoma (HNSCC) is a frequently fatal heterogeneous
disease. Beyond the role of human papilloma virus (HPV), no validated molecular …
disease. Beyond the role of human papilloma virus (HPV), no validated molecular …
Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology
Significant innovations in next-generation sequencing techniques and bioinformatics tools
have impacted our appreciation and understanding of RNA. Practical RNA sequencing …
have impacted our appreciation and understanding of RNA. Practical RNA sequencing …
Leveraging transcript quantification for fast computation of alternative splicing profiles
GP Alamancos, A Pagès, JL Trincado, N Bellora… - Rna, 2015 - rnajournal.cshlp.org
Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …