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 …
Evolution to the rescue: using comparative genomics to understand long non-coding RNAs
I Ulitsky - Nature Reviews Genetics, 2016 - nature.com
Long non-coding RNAs (lncRNAs) have emerged in recent years as major players in a
multitude of pathways across species, but it remains challenging to understand which of …
multitude of pathways across species, but it remains challenging to understand which of …
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
High-throughput sequencing of mRNA (RNA-seq) has become the standard method for
measuring and comparing the levels of gene expression in a wide variety of species and …
measuring and comparing the levels of gene expression in a wide variety of species and …
[HTML][HTML] Cerebral organoids recapitulate epigenomic signatures of the human fetal brain
Organoids derived from human pluripotent stem cells recapitulate the early three-
dimensional organization of the human brain, but whether they establish the epigenomic …
dimensional organization of the human brain, but whether they establish the epigenomic …
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
Endogenous retroviruses (ERVs) are abundant in mammalian genomes and contain
sequences modulating transcription. The impact of ERV propagation on the evolution of …
sequences modulating transcription. The impact of ERV propagation on the evolution of …
–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 …
High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation
The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs)
contribute to the specialized functions of cells within an organ is poorly understood. We …
contribute to the specialized functions of cells within an organ is poorly understood. We …
[HTML][HTML] Next-generation biology: sequencing and data analysis approaches for non-model organisms
As sequencing technologies become more affordable, it is now realistic to propose studying
the evolutionary history of virtually any organism on a genomic scale. However, when …
the evolutionary history of virtually any organism on a genomic scale. However, when …
Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
S Oikonomopoulos, YC Wang, H Djambazian… - Scientific reports, 2016 - nature.com
To assess the performance of the Oxford Nanopore Technologies MinION sequencing
platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix …
platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix …
CANTATAdb: a collection of plant long non-coding RNAs
MW Szcześniak, W Rosikiewicz… - Plant and Cell …, 2016 - academic.oup.com
Long non-coding RNAs (lncRNAs) represent a class of potent regulators of gene expression
that are found in a wide array of eukaryotes; however, our knowledge about these molecules …
that are found in a wide array of eukaryotes; however, our knowledge about these molecules …