Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

(2013) H. Maamar et al.   GENES & DEVELOPMENT

Morphological and molecular markers are correlated with maturation-competence of human oocytes

(2013) M. Levi et al.   HUMAN REPRODUCTION

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

(2013) Alex K. Shalek et al.   NATURE

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments

(2013) Quin F Wills et al.   NATURE BIOTECHNOLOGY

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Upregulation of lncRNAs at 13q14.3 in Leukemia Is Linked to the In Cis Downregulation of a Gene Cluster That Targets NF-kB

(2013) Angela Garding et al.   PLoS Genetics

Preimplantation genetic diagnosis: recent triumphs and remaining challenges

(2012) Sioban B SenGupta et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Decapping of Long Noncoding RNAs Regulates Inducible Genes

(2012) Sarah Geisler et al.   MOLECULAR CELL

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

(2012) Zhipeng Qu et al.   PLoS One

Identification and Comparative Analysis of ncRNAs in Human, Mouse and Zebrafish Indicate a Conserved Role in Regulation of Genes Expressed in Brain

(2012) Zhipeng Qu et al.   PLoS One

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

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

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

(2011) Tiffany Hung et al.   NATURE GENETICS

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

(2010) Chol-Hee Jung et al.   BMC GENOMICS

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Assessment of embryo viability in assisted reproductive technology: shortcomings of current approaches and the emerging role of metabolomics

(2008) Jason G Bromer et al.   CURRENT OPINION IN OBSTETRICS & GYNECOLOGY

Determination of microRNAs in mouse preimplantation embryos by microarray

(2008) Yanhong Yang et al.   DEVELOPMENTAL DYNAMICS

Assisted reproductive technology in Europe, 2004: results generated from European registers by ESHRE

(2008) A. Nyboe Andersen et al.   HUMAN REPRODUCTION

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE