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List of works by John L. Rinn

"Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription

scientific article

'Lnc'-ing enhancers to MYC regulation

scientific article published on 29 April 2014

'Oming in on RNA-protein interactions

scientific article published on 31 January 2014

A Keystone for ncRNA ⬇️

scientific article published on May 25, 2012

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.

scientific article

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

scientific article

A dermal HOX transcriptional program regulates site-specific epidermal fate

scientific article

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs

scientific article published on 20 June 2011

A histone H3 lysine 27 demethylase regulates animal posterior development

scientific article

A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response

scientific journal article

A systems biology approach to anatomic diversity of skin

scientific article published on April 2008

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

scientific article (publication date: May 2010)

Anatomic demarcation by positional variation in fibroblast gene expression programs

scientific article published in July 2006

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

scientific article published on 03 May 2016

CORRECTION

CREB binds to multiple loci on human chromosome 22.

scientific article published on May 2004

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

scientific article published on 07 December 2016

Chromatin signature of embryonic pluripotency is established during genome activation

scientific article published on 24 March 2010

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

scientific article (publication date: 12 March 2009)

Computational analysis of noncoding RNAs

scientific article

Control of somatic tissue differentiation by the long non-coding RNA TINCR.

scientific article published on 2 December 2012

DNA methylation and epigenetic control of cellular differentiation

scientific article published on 20 October 2010

DNMT1-interacting RNAs block gene-specific DNA methylation

scientific article published on 09 October 2013

DeCoN: Genome-wide Analysis of In Vivo Transcriptional Dynamics during Pyramidal Neuron Fate Selection in Neocortex

DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex

scientific article published on 31 December 2014

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research

Differential analysis of gene regulation at transcript resolution with RNA-seq

scientific article (publication date: 2013)

Differential contribution of steady-state RNA and active transcription in chromatin organization

scientific article published on 26 August 2019

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

scientific article

Discovery and annotation of long noncoding RNAs

scientific article published in January 2015

Dissecting neural differentiation regulatory networks through epigenetic footprinting

scientific article published on 24 December 2014

Distribution of NF-kappaB-binding sites across human chromosome 22

scientific article

Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs

scientific article

Dynamic changes during the treatment of pancreatic cancer

scientific article published on 13 February 2018

Enhancers in the Peril lincRNA locus regulate distant but not local genes

article

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

scholarly article published in Nature Biotechnology

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Expression of Shal potassium channel subunits in the adult and developing cochlear nucleus of the mouse

scientific article published in September 2000

Function and evolution of local repeats in the Firre locus

scientific article published on 24 March 2016

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

scientific article

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

scientific journal article

Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2

scientific article published on 01 November 2018

Genome regulation by long noncoding RNAs.

scientific article

Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy

scientific article

Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs

scientific article

Genome-wide measurement of RNA secondary structure in yeast

scientific article

Genomics in 2011: challenges and opportunities

scientific article published on 28 December 2011

Global identification of human transcribed sequences with genome tiling arrays

scientific article (publication date: 24 December 2004)

Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA.

scientific article

HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells

scientific article published on July 2009

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells

scientific article published on February 2009

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

High-throughput identification of RNA nuclear enrichment sequences

scientific article published on 15 January 2018

Identification of proteins binding coding and non-coding human RNAs using protein microarrays

scientific article

Identifying recent adaptations in large-scale genomic data

scientific article

Improving RNA-Seq expression estimates by correcting for fragment bias

scientific article

In vivo Ebola virus infection leads to a strong innate response in circulating immune cells

scientific article published on 05 September 2016

In vivo and deletion elucidates roles for autosomal gene regulation

scientific article published on 18 November 2019

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

scientific article published in July 2015

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer

scientific article published on 15 March 2016

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

scientific article (publication date: 15 September 2011)

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

scientific article published on 16 April 2015

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.

scientific article published on 27 February 2018

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.

scientific article

In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements

scientific article published on 10 August 2016

LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer

scientific article published on 10 September 2016

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

scientific article

Large non-coding RNAs: missing links in cancer? ⬇️

scientific article published on August 20, 2010

Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies

scientific article

Linking RNA biology to lncRNAs

scientific article

Linking long noncoding RNA to drug resistance

scientific article published on 10 October 2019

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking.

scientific article published on 14 December 2017

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

scientific article

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

scientific article

Long noncoding RNAs regulate adipogenesis

scientific article

Major molecular differences between mammalian sexes are involved in drug metabolism and renal function

scientific article published in June 2004

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

scientific article

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

scientific article

Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire

scientific article published on May 2008

Mining data from 1000 genomes to identify the causal variant in regions under positive selection.

scientific article published on 11 October 2010

Modular regulatory principles of large non-coding RNAs

scientific article (publication date: 15 February 2012)

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

scientific article (publication date: 31 December 2013)

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

scientific article

Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body

scientific article published on 24 January 2008

Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart

scientific article published on 01 January 2021

Neat1 is a p53-inducible lincRNA essential for transformation suppression

scientific article published on 11 July 2017

Non-coding RNAs as regulators of embryogenesis

scientific article

Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention

scientific article published on 03 June 2021

Peptidomic discovery of short open reading frame-encoded peptides in human cells.

scientific article

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

scientific article

Poly-combing the genome for RNA.

scientific article published in December 2013

Programming human pluripotent stem cells into white and brown adipocytes.

scientific article

RNA Function. RNA and dynamic nuclear organization

scientific article

RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells

scientific article published on 06 July 2020

RNA traffic control of chromatin complexes

scientific article

RNA-protein interactions in human health and disease

scientific article

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

scientific article

Ras/Erk MAPK signaling in epidermal homeostasis and neoplasia

scientific article published on 04 September 2007

Reorganization of chromosomal interactions in the 2q37-deletion syndrome

scientific article published on 19 June 2018

Resolving mechanisms of immune-mediated disease in primary CD4 T cells

scientific article published on 01 April 2020

Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs

scientific article published on 22 May 2013

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

scientific article

Sequences to systems

scientific article published on 25 May 2010

Sexual dimorphism in mammalian gene expression

scientific article

Silent pericentromeric repeats speak out.

scientific article

Single-cell imaging reveals unexpected heterogeneity of telomerase reverse transcriptase expression across human cancer cell lines

scientific article published on 26 August 2019

Sixty years of genome biology

scientific article published on 25 April 2013

Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING).

scientific article published on 8 January 2018

Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain

scientific article

Spontaneous autoimmunity prevented by thymic expression of a single self-antigen

scientific article

Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA.

scientific article published on 13 June 2015

Suppression of progenitor differentiation requires the long noncoding RNA ANCR.

scientific article published on 2 February 2012

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

scientific article published on 22 November 2011

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

scientific article

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

scientific article published on 30 March 2015

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

scientific article published on 13 November 2019

The Sox2 transcription factor binds RNA

scientific article published on 14 April 2020

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

scientific article published on 23 March 2014

The histone chaperone CAF-1 safeguards somatic cell identity

scientific article

The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis

scientific article published on 25 April 2013

The multilayered complexity of ceRNA crosstalk and competition

scientific article

The reality of pervasive transcription

scientific article

The transcriptional activity of human Chromosome 22

scientific article

To repress or not to repress: This is the guardian's question ⬇️

scientific article published on May 19, 2011

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

scientific article

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

scientific article published on 27 November 2020

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

scientific article published on 09 May 2013

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

scientific article published on 2 February 2016

Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions

scientific article

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

scientific article published on 26 November 2012

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

scientific article

Visualization of lncRNA by single-molecule fluorescence in situ hybridization

scientific article published on January 2015

Widespread RNA binding by chromatin-associated proteins

scientific article published on 16 February 2016

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

scientific journal article

lincRNAs act in the circuitry controlling pluripotency and differentiation

scientific article (publication date: 28 August 2011)

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation.

scientific article published on 6 September 2017

lncRNAs: linking RNA to chromatin

scientific article

p53 regulates enhancer accessibility and activity in response to DNA damage

scientific article published on September 2017

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