High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

Integrated transcriptome analysis of mouse spermatogenesis

(2014) Gennady Margolin et al.   BMC GENOMICS

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Stability, delivery and functions of human sperm RNAs at fertilization

(2013) Edward Sendler et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis

(2013) Asta Laiho et al.   PLoS One

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts

(2012) C. S. Lee et al.   BLOOD

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Conceptual approaches for lncRNA drug discovery and future strategies

(2012) Deeksha Bhartiya et al.   Expert Opinion on Drug Discovery

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

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

(2012) T. Derrien et al.   GENOME RESEARCH

Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility

(2012) Frédéric Chalmel et al.   HUMAN REPRODUCTION

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

(2012) Cole Trapnell et al.   Nature Protocols

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Characterization of Novel Paternal ncRNAs at the Plagl1 Locus, Including Hymai, Predicted to Interact with Regulators of Active Chromatin

(2012) Isabel Iglesias-Platas et al.   PLoS One

Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs

(2012) F. Niazi et al.   RNA

Meiosis-Specific Noncoding RNA Mediates Robust Pairing of Homologous Chromosomes in Meiosis

(2012) D.-Q. Ding et al.   SCIENCE

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

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

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

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

Xist regulation and function eXplored

(2011) Daphne B. Pontier et al.   HUMAN GENETICS

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

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

Chromatoid body and small RNAs in male germ cells

(2011) Oliver Meikar et al.   REPRODUCTION

Long noncoding RNA in genome regulation

(2011) Tiffany Hung et al.   RNA Biology

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

The Long Noncoding RNA, Jpx, Is a Molecular Switch for X Chromosome Inactivation

(2010) Di Tian et al.   CELL

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

HOTAIR: Flight of noncoding RNAs in cancer metastasis

(2010) Yue Wan et al.   CELL CYCLE

RNA traffic control of chromatin complexes

(2010) Magdalena J Koziol et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

An Integrative Approach to Genomic Introgression Mapping

(2010) Andrew J. Severin et al.   PLANT PHYSIOLOGY

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

(2010) A. Lardenois et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Long noncoding RNAs: functional surprises from the RNA world

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

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Long non-coding RNAs: insights into functions

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

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

(2008) Frédéric Chalmel et al.   BMC BIOINFORMATICS

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Paternal contributions: New functional insights for spermatozoal RNA

(2008) Claudia Lalancette et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control

(2008) Yi Zhao et al.   TRENDS IN GENETICS