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Flynn Lab

Research
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All Publications
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Featured
   Flynn RA, Smith BAH, Johnson AG, Pedram K, George BM, Malaker SA, Majzoub K, Carette JE, Bertozzi CR  Mammalian Y RNAs are modified at discrete guanosine residues with N-glycans   bioRxiv.  September 2019    bioRxiv
Oct 1, 2019
Oct 1, 2019

Flynn RA, Smith BAH, Johnson AG, Pedram K, George BM, Malaker SA, Majzoub K, Carette JE, Bertozzi CR

Mammalian Y RNAs are modified at discrete guanosine residues with N-glycans

bioRxiv. September 2019

bioRxiv

Oct 1, 2019
    Tomlin FM*, Gerling-Driessen UIM*, Liu YC,  Flynn RA , Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR   Inhi
Oct 28, 2017
Oct 28, 2017

 

Tomlin FM*, Gerling-Driessen UIM*, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR

Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity

ACS Central Science. October 2017

Pubmed    PDF

Oct 28, 2017
 Chan D, Feng C, Zhen Y,  Flynn RA , Spitale RC   Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts   Biochemistry. April 2017   Pubmed    &
Oct 28, 2017
Oct 28, 2017

Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC

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

Biochemistry. April 2017

Pubmed     PDF
 

Oct 28, 2017
Featured
 Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J,  Flynn RA , Kundaje A, Khavari PA, Marson A, Corn JE, Quert
Oct 28, 2017
Oct 28, 2017

Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

Nat Genetics. November 2017

Pubmed     PDF

Oct 28, 2017
 Simsek D, Tiu GC,  Flynn RA , Byeon GW, Leppek K, Xu AF, Chang HY, Barna M   The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity    Cell . June 2017   Pubmed       PDF
Oct 28, 2017
Oct 28, 2017

Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M

The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity

Cell. June 2017

Pubmed     PDF

Oct 28, 2017
 Lee B,  Flynn RA , Kadina A, Guo JK, Kool ET, Chang HY.   Comparison of SHAPE Reagents for Mapping RNA Structures Inside Living Cells    RNA.  December 2016   Pubmed       PDF
Dec 24, 2016
Dec 24, 2016

Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY.

Comparison of SHAPE Reagents for Mapping RNA Structures Inside Living Cells

RNA. December 2016

Pubmed     PDF

Dec 24, 2016
HiChIP
Dec 24, 2016
HiChIP
Dec 24, 2016

Mumbach MR*, Rubin AJ*, Flynn RA*, Dai C, Khavari PA, Greenleaf WJ, Chang HY.

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

Nature Methods. November 2016

Pubmed     PDF

Dec 24, 2016
DINO
Dec 24, 2016
DINO
Dec 24, 2016

Schmitt AM*, Garcia JT*, Hung T*, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY.

An inducible long noncoding RNA amplifies DNA damage signaling

Nature Genetics. November 2016

Pubmed     PDF

Dec 24, 2016
Skin Youthfulness
Dec 24, 2016
Skin Youthfulness
Dec 24, 2016

Xu J, Spitale RC, Guan L, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang AL.

Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing

PLoS One. November 2016

Pubmed     PDF

Dec 24, 2016
PARIS
May 12, 2016
PARIS
May 12, 2016

Lu Z*, Zhang QC*, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY

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

Cell. May 2016

Pubmed     PDF

 

May 12, 2016
 Zarnegar BJ,  Flynn RA , Shen Y, Do DT, Chang HY, Khavari PA.   Ultraefficient irCLIP platform for characterization of protein-RNA interactions.    Nature Methods.  April 2016   Highlighted in     N  ature Methods, News and Views  and  Molecular Cel
May 12, 2016
May 12, 2016

Zarnegar BJ, Flynn RA, Shen Y, Do DT, Chang HY, Khavari PA.

Ultraefficient irCLIP platform for characterization of protein-RNA interactions.

Nature Methods. April 2016

Highlighted in Nature Methods, News and Views and Molecular Cell, Technology Preview

Pubmed     PDF

May 12, 2016
 Tan JL, Fogley RD,  Flynn RA , Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price D
May 12, 2016
May 12, 2016

Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI.

Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma.

Molecular Cell. April 2016

Pubmed     PDF

May 12, 2016
 Oh S*,  Flynn RA* , Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfiste
May 12, 2016
May 12, 2016

Oh S*, Flynn RA*, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ.

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.

Oncotarget. 2016

Pubmed     PDF

May 12, 2016
Featured
  Flynn RA *, Almada AE*, Zamudio JR, Sharp PA.   Antisense RNA polymerase II divergent transcripts are P-TEFb dependent substrates for the RNA exosome.    PNAS . July 2011   Pubmed       PDF
Feb 15, 2016
Feb 15, 2016

Flynn RA*, Almada AE*, Zamudio JR, Sharp PA.

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

PNAS. July 2011

Pubmed     PDF

Feb 15, 2016
 Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM,  Flynn RA , Cavenee WK, Furnari FB, White FM.  Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth.   Mol Bi
Feb 15, 2016
Feb 15, 2016

Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee WK, Furnari FB, White FM.

Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth.

Mol Biosystems. May 2010

Pubmed     PDF

Feb 15, 2016
 Rahl PB, Lin CY, Seila AC,  Flynn RA , McCuine S, Burge CB, Sharp PA, Young RA.   c-Myc regulates transcriptional pause release.    Cell . April 2010   Pubmed       PDF
Feb 15, 2016
Feb 15, 2016

Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA.

c-Myc regulates transcriptional pause release.

Cell. April 2010

Pubmed     PDF

Feb 15, 2016
 Seila AC, Calabrese M, Levine SS, Yeo GW, Rahl PB,  Flynn RA , Young RA, Sharp PA.   Divergent transcription from active promoters.    Science . December 2008   Pubmed       PDF    
Feb 15, 2016
Feb 15, 2016

Seila AC, Calabrese M, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Divergent transcription from active promoters.

Science. December 2008

Pubmed     PDF

 

Feb 15, 2016
 Huang PH, Mukasa A, Bonavia R,  Flynn RA , Brewer ZE, Cavenee WK, Furnari FB, White FM.   Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma.    PNAS . July 2007   Pubmed  &nbs
Feb 15, 2016
Feb 15, 2016

Huang PH, Mukasa A, Bonavia R, Flynn RA, Brewer ZE, Cavenee WK, Furnari FB, White FM.

Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma.

PNAS. July 2007

Pubmed     PDF

Feb 15, 2016
 Tuli R,  Flynn RA , Brill KL, Sabol JL, Usuki KY, Rosenberg AL.    Diagnosis, treatment, and management of breast cancer in previously augmented women.    Breast J . August 2006   Pubmed       PDF
Feb 15, 2016
Feb 15, 2016

Tuli R, Flynn RA, Brill KL, Sabol JL, Usuki KY, Rosenberg AL. 

Diagnosis, treatment, and management of breast cancer in previously augmented women.

Breast J. August 2006

Pubmed     PDF

Feb 15, 2016
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The scientist does not study nature because it is useful; they study it because they delight in it, and they delight in it because it is beautiful. If nature were not beautiful, it would not be worth knowing, and if nature were not worth knowing , life would not be worth living.
-Henri Poincare