List of works - Ryan Flynn

7SK-BAF axis controls pervasive transcription at enhancers

scientific article published on 15 February 2016

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

scientific article (publication date: 7 April 2011)

Active chromatin and noncoding RNAs: an intimate relationship

scientific article published on 07 December 2011

An RNA-centric dissection of host complexes controlling flavivirus infection

scientific article published on 05 August 2019

An inducible long noncoding RNA amplifies DNA damage signaling.

scientific article published on 26 September 2016

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

scientific article

Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts

scientific article

Comparison of SHAPE reagents for mapping RNA structures inside living cells

scientific article published on 22 November 2016

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

scientific article published on 2 December 2012

DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

scientific article published on 16 December 2015

Dissecting noncoding and pathogen RNA-protein interactomes

scientific article

Divergent transcription from active promoters

scientific article (publication date: 19 December 2008)

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

scientific article published on 12 February 2014

Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

scientific article published on 13 December 2019

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

scientific article

HiChIRP reveals RNA-associated chromosome conformation

scientific article published on 27 May 2019

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

scientific article

Landscape and variation of RNA secondary structure across the human transcriptome

scientific article

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation

scientific article

Long noncoding RNAs in cell-fate programming and reprogramming

scientific article

Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

scientific article published on 25 November 2020

Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures

scientific article published on 27 July 2020

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

scientific article

RNA SHAPE analysis in living cells

scientific article published on 25 November 2012

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

scientific article

RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells

scientific article published on 30 March 2020

RNA structural analysis by evolving SHAPE chemistry

scientific article

Small RNAs are modified with N-glycans and displayed on the surface of living cells

scientific article published on 17 May 2021

Structural imprints in vivo decode RNA regulatory mechanisms

scientific article published on 18 March 2015

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

scientific article published on 06 October 2020

Systematic discovery of Xist RNA binding proteins

scientific article

The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C

scientific article published on 01 December 2021

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

scientific article

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

scientific article

Zika Virus Infection Prevents Host mRNA Nuclear Export by Disrupting UPF1 Function

scientific article

c-Myc regulates transcriptional pause release

scientific article

fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins

scientific article published on 25 August 2021

irCLIP platform for efficient characterization of protein-RNA interactions

scientific article published on 25 April 2016

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells

scientific article

List of works by Ryan Flynn

7SK-BAF axis controls pervasive transcription at enhancers

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

Active chromatin and noncoding RNAs: an intimate relationship

An RNA-centric dissection of host complexes controlling flavivirus infection

An inducible long noncoding RNA amplifies DNA damage signaling.

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts

Comparison of SHAPE reagents for mapping RNA structures inside living cells

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

DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

Dissecting noncoding and pathogen RNA-protein interactomes

Divergent transcription from active promoters

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

HiChIRP reveals RNA-associated chromosome conformation

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

Landscape and variation of RNA secondary structure across the human transcriptome

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation

Long noncoding RNAs in cell-fate programming and reprogramming

Progenitor identification and SARS-CoV-2 infection in human distal lung organoids

Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

RNA SHAPE analysis in living cells

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells

RNA structural analysis by evolving SHAPE chemistry

Small RNAs are modified with N-glycans and displayed on the surface of living cells

Structural imprints in vivo decode RNA regulatory mechanisms

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

Systematic discovery of Xist RNA binding proteins

The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

Zika Virus Infection Prevents Host mRNA Nuclear Export by Disrupting UPF1 Function

c-Myc regulates transcriptional pause release

fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins

irCLIP platform for efficient characterization of protein-RNA interactions

m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells