Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells

Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse

(2017) Xiaoyong Li et al.   Scientific Reports

Production of offspring from a germline stem cell line derived from prepubertal ovaries of germline reporter mice

(2016) Chen Zhang et al.   MOLECULAR HUMAN REPRODUCTION

The biogenesis and emerging roles of circular RNAs

(2016) Ling-Ling Chen   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive identification of internal structure and alternative splicing events in circular RNAs

(2016) Yuan Gao et al.   Nature Communications

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data

(2016) Kun Sun et al.   BMC GENOMICS

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor

(2015) Yehoshua Enuka et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq

(2015) Yafang Li et al.   PLoS One

RNA-seq of 272 gliomas revealed a novel, recurrentPTPRZ1-METfusion transcript in secondary glioblastomas

(2014) Zhao-Shi Bao et al.   GENOME RESEARCH

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development

(2013) Jin Sun et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

National, Regional, and Global Trends in Infertility Prevalence Since 1990: A Systematic Analysis of 277 Health Surveys

(2012) Maya N. Mascarenhas et al.   PLOS MEDICINE

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

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

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Long noncoding RNAs: functional surprises from the RNA world

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

Production of offspring from a germline stem cell line derived from neonatal ovaries

(2009) Kang Zou et al.   NATURE CELL BIOLOGY

Long non-coding RNAs: insights into functions

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

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS