Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs (Q36538489)

14 August 2017

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs (English)

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Aviv Regev

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14 August 2017

Sabah Kadri

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Xiaopeng Zhu

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Xiaopeng Zhu

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Manuel Garber

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Manuel Garber

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14 August 2017

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Mitchell Guttman

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14 August 2017

Jenny Chen

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Alexander A Shishkin

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Itay Maza

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2 February 2016

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https://scigraph.springernature.com/pub.10.1186/s13059-016-0880-9

14 August 2017

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cites work

Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

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Simultaneous generation of many RNA-seq libraries in a single reaction

30 September 2017

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The landscape of long noncoding RNAs in the human transcriptome

30 September 2017

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The evolution of lncRNA repertoires and expression patterns in tetrapods

30 September 2017

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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

30 September 2017

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Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

30 September 2017

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Multiple knockout mouse models reveal lincRNAs are required for life and brain development

30 September 2017

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30 September 2017

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30 September 2017

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RefSeq: an update on mammalian reference sequences

30 September 2017

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Differential L1 regulation in pluripotent stem cells of humans and apes.

30 September 2017

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A long noncoding RNA mediates both activation and repression of immune response genes

30 September 2017

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Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins

30 September 2017

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PRISM offers a comprehensive genomic approach to transcription factor function prediction

30 September 2017

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Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

30 September 2017

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CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment

30 September 2017

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

30 September 2017

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GENCODE: the reference human genome annotation for The ENCODE Project

30 September 2017

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Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

30 September 2017

1 reference

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BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration

30 September 2017

1 reference

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

30 September 2017

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Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

30 September 2017

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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

30 September 2017

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Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

30 September 2017

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The evolution of gene expression levels in mammalian organs

30 September 2017

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A high-resolution map of human evolutionary constraint using 29 mammals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

lincRNAs act in the circuitry controlling pluripotency and differentiation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

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

30 September 2017

1 reference

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RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

30 September 2017

1 reference

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Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

30 September 2017

1 reference

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Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs

30 September 2017

1 reference

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

30 September 2017

1 reference

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BEDTools: a flexible suite of utilities for comparing genomic features

30 September 2017

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Identifying novel constrained elements by exploiting biased substitution patterns

30 September 2017

1 reference

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Metastable pluripotent states in NOD-mouse-derived ESCs

30 September 2017

1 reference

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Klf4 reverts developmentally programmed restriction of ground state pluripotency

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Dissecting direct reprogramming through integrative genomic analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

New cell lines from mouse epiblast share defining features with human embryonic stem cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

The UCSC Genome Browser Database: update 2006

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

A strategy for probing the function of noncoding RNAs finds a repressor of NFAT

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Human and mouse gene structure: comparative analysis and application to exon prediction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Deletions of the steroid sulphatase gene in "classical" X-linked ichthyosis and in X-linked ichthyosis associated with Kallmann syndrome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

The product of the H19 gene may function as an RNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Comparative epigenomic annotation of regulatory DNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Integrating genomic homology into gene structure prediction.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Derivation of novel human ground state naive pluripotent stem cells

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

21 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13059-016-0880-9

The conserved exon method for gene finding

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4739325

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems

21 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13059-016-0880-9

10.1186/S13059-016-0880-9

21 January 2018

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14 August 2017

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14 August 2017

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