LncRNA-ID: Long non-coding RNA IDentification using balanced random forests

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages

(2014) Juan-José Vasquez et al.   NUCLEIC ACIDS RESEARCH

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

(2014) Yuan Zhang et al.   PLoS Computational Biology

A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads

(2013) Yuan Zhang et al.   BIOINFORMATICS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

A long non-coding RNA promotes full activation of adult gene expression in the chicken α-globin domain

(2013) Cristian Arriaga-Canon et al.   Epigenetics

CoRAL: predicting non-coding RNAs from small RNA-sequencing data

(2013) Yuk Yee Leung et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Sequence and Expression Characteristics of Long Noncoding RNAs in Honey Bee Caste Development – Potential Novel Regulators for Transgressive Ovary Size

(2013) Fernanda C. Humann et al.   PLoS One

Inheritable and Precise Large Genomic Deletions of Non-Coding RNA Genes in Zebrafish Using TALENs

(2013) Yun Liu et al.   PLoS One

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Random forests for genomic data analysis

(2012) Xi Chen et al.   GENOMICS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner et al.   PLoS One

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

(2011) Yuan Zhang et al.   BMC BIOINFORMATICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

La enhances IRES-mediated translation of laminin B1 during malignant epithelial to mesenchymal transition

(2011) Michaela Petz et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA in genome regulation

(2011) Tiffany Hung et al.   RNA Biology

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Length of the ORF, position of the first AUG and the Kozak motif are important factors in potential dual-coding transcripts

(2010) Heng Xu et al.   CELL RESEARCH

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Long noncoding RNAs: functional surprises from the RNA world

(2009) J. E. Wilusz et al.   GENES & DEVELOPMENT

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

(2008) Jiansheng Wu et al.   BIOINFORMATICS

Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation

(2008) Chuanhua Xing et al.   NUCLEIC ACIDS RESEARCH

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology