ShortStack: comprehensive annotation and quantification of small RNA genes.

By Michael J. Axtell. RNA: A publication of the RNA Society, 2013

446 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/9a7f93059d87ba6d4fe9814397f1e64b9db19012

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cancer Research

1. Ana Conesa
2. Sonia Tarazona
3. Ali Mortazavi
4. Seth Schobel
5. Christopher D. Town
6. Agnes P. Chan
7. Vivek Krishnakumar
8. Xuegong Zhang

In Molecular Biology

1. Laura L. Elo
2. Sonia Tarazona
3. Ana Conesa
4. David Gomez-Cabrero
5. Pedro Madrigal
6. Ali Mortazavi
7. M. Szcześniak
8. Seth Schobel

In Plant Science

1. Ali Mortazavi
2. Seth Schobel
3. Christopher D. Town
4. Agnes P. Chan
5. Vivek Krishnakumar
6. Chia-Yi Cheng

Citations in the corpus

• Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “We used ShortStack (Axtell, 2013) to identify de novo small RNA clusters (miRNA search disabled,—nohp).”
• A survey of best practices for RNA-seq data analysis (2016, methodology): “Tools such as miRTools 2.0 [96], ShortStack [104], and iMir [105] also exist for comprehensive annotation of sRNA libraries and for identification of diverse classes of sRNAs.”