Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

(2015) Victoria Villegas et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

BioServices: a common Python package to access biological Web Services programmatically

(2013) Thomas Cokelaer et al.   BIOINFORMATICS

Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing

(2013) Xi Wang et al.   BMC BIOINFORMATICS

Regulatory Non-Coding RNAs in Pluripotent Stem Cells

(2013) Alessandro Rosa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detection of non-coding RNA in bacteria and archaea using the DETR’PROK Galaxy pipeline

(2013) Claire Toffano-Nioche et al.   METHODS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

DAVID-WS: a stateful web service to facilitate gene/protein list analysis

(2012) X. Jiao et al.   BIOINFORMATICS

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

The functional role of long non-coding RNA in human carcinomas

(2011) Ewan A Gibb et al.   Molecular Cancer

Mechanisms and functions of Hedgehog signalling across the metazoa

(2011) Philip W. Ingham et al.   NATURE REVIEWS GENETICS

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

Role of H3K27 methylation in the regulation of lncRNA expression

(2010) Susan C Wu et al.   CELL RESEARCH

Altered antisense-to-sense transcript ratios in breast cancer

(2010) R. Maruyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

(2009) Roberto T Arrial et al.   BMC BIOINFORMATICS

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH