HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Evolution of the unspliced transcriptome

(2015) Jan Engelhardt et al.   BMC EVOLUTIONARY BIOLOGY

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Heightened potency of human pluripotent stem cell lines created by transient BMP4 exposure

(2015) Ying Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome

(2015) Ana C Ayupe et al.   RNA Biology

Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development

(2015) Virpi Töhönen et al.   Nature Communications

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes

(2015) Michael S. Werner et al.   Cell Reports

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

RETRACTED: Long non-coding RNAINXSis a critical mediator ofBCL-XSinduced apoptosis

(2014) Carlos DeOcesano-Pereira et al.   NUCLEIC ACIDS RESEARCH

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

(2014) Aurélie Kapusta et al.   TRENDS IN GENETICS

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Principles of nucleation of H3K27 methylation during embryonic development

(2013) S. J. van Heeringen et al.   GENOME RESEARCH

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations

(2013) Angela A Fachel et al.   Molecular Cancer

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

The Translational Landscape of the Mammalian Cell Cycle

(2013) Craig R. Stumpf et al.   MOLECULAR CELL

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation

(2013) Felipe C. Beckedorff et al.   PLoS Genetics

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

(2013) Ana C Marques et al.   GENOME BIOLOGY

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts

(2012) Marco Magistri et al.   TRENDS IN GENETICS

Comparative Transcriptome Analysis of Human Trophectoderm and Embryonic Stem Cell-Derived Trophoblasts Reveal Key Participants in Early Implantation1

(2011) Lusine Aghajanova et al.   BIOLOGY OF REPRODUCTION

Reversal of epigenetic silencing of AP-2alpha results in increased zinc uptake in DU-145 and LNCaP prostate cancer cells

(2011) Peter B. Makhov et al.   CARCINOGENESIS

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

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

Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

(2011) Ana C Tahira et al.   Molecular Cancer

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Pervasive transcription constitutes a new level of eukaryotic genome regulation

(2009) Julia Berretta et al.   EMBO REPORTS

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

(2009) Da Wei Huang et al.   Nature Protocols