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 …
Technology dictates algorithms: recent developments in read alignment
Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …
analysis pipelines. Computational algorithms for read alignment have evolved in …
Tools for mapping high-throughput sequencing data
Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is
the alignment (mapping) of the generated reads to a reference sequence. To accomplish …
the alignment (mapping) of the generated reads to a reference sequence. To accomplish …
The cardiac transcription network modulated by Gata4, Mef2a, Nkx2. 5, Srf, histone modifications, and microRNAs
J Schlesinger, M Schueler, M Grunert, JJ Fischer… - PLoS …, 2011 - journals.plos.org
The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the
interaction between different molecular levels, involving epigenetic, transcriptional, and post …
interaction between different molecular levels, involving epigenetic, transcriptional, and post …
[HTML][HTML] The SeqAn C++ template library for efficient sequence analysis: A resource for programmers
Background The use of novel algorithmic techniques is pivotal to many important problems
in life science. For example the sequencing of the human genome (Venter et al., 2001) …
in life science. For example the sequencing of the human genome (Venter et al., 2001) …
High‐throughput deep sequencing shows that micro RNA s play important roles in switchgrass responses to drought and salinity stress
Micro RNA s (mi RNA s) are an important class of small regulatory RNA s. The goal of this
study was to analyse stress‐responsive mi RNA s in switchgrass (P anicum virgatum), the …
study was to analyse stress‐responsive mi RNA s in switchgrass (P anicum virgatum), the …
The elucidation of stress memory inheritance in Brassica rapa plants
Plants are able to maintain the memory of stress exposure throughout their ontogenesis and
faithfully propagate it into the next generation. Recent evidence argues for the epigenetic …
faithfully propagate it into the next generation. Recent evidence argues for the epigenetic …
Lambda: the local aligner for massive biological data
H Hauswedell, J Singer, K Reinert - Bioinformatics, 2014 - academic.oup.com
Motivation: Next-generation sequencing technologies produce unprecedented amounts of
data, leading to completely new research fields. One of these is metagenomics, the study of …
data, leading to completely new research fields. One of these is metagenomics, the study of …
Evaluation of microRNA alignment techniques
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses
considerable challenges due to their short length (∼ 21 nucleotides [nt]) as well as the large …
considerable challenges due to their short length (∼ 21 nucleotides [nt]) as well as the large …
The Hot Pepper (Capsicum annuum) MicroRNA Transcriptome Reveals Novel and Conserved Targets: A Foundation for Understanding MicroRNA Functional Roles …
DG Hwang, JH Park, JY Lim, D Kim, Y Choi, S Kim… - PloS one, 2013 - journals.plos.org
MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which
play important roles in regulating gene expression in plants. Although many miRNA studies …
play important roles in regulating gene expression in plants. Although many miRNA studies …