Co-authored publications with mentees

Samie R Jaffrey, MD, PhD · 49 publications across 19 mentees

CSV Word

PhD mentee

A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins.
Nucleic acids research · 2026
SRSamie R JaffreyMOMaxim OleynikovKSKi Sung Park AHAashiq H. MirzaQHQian Hou+1 more →
PMID: 42531073PMCID: PMC13421773DOI
With Maxim Oleynikov · Pharmacology (PhD)
A portable poison exon for small-molecule control of mammalian gene expression.
Nature methods · 2025
SRSamie R JaffreyMOMaxim OleynikovQHQian HouXAXiaohan Alex MeiLDLinghao Dong+1 more →
PMID: 41184552PMCID: PMC13102273DOI2 citations
With Maxim Oleynikov · Pharmacology (PhD)
A portable poison exon for small-molecule control of mammalian gene expression.
Nature methods · 2025
SRSamie R JaffreyLDLinghao DongQHQian HouMOMaxim OleynikovXAXiaohan Alex Mei+1 more →
PMID: 41184552PMCID: PMC13102273DOI2 citations
With Linghao Dong · Pharmacology (PhD)
RNA tertiary structure and conformational dynamics revealed by BASH MaP.
eLife · 2024
SRSamie R JaffreyMOMaxim Oleynikov
PMID: 39625751PMCID: PMC11614387DOI
With Maxim Oleynikov · Pharmacology (PhD)
A circular split nanoluciferase reporter for validating and screening putative internal ribosomal entry site elements.
RNA (New York, N.Y.) · 2024
SRSamie R JaffreyMJMildred J Unti
PMID: 39103230PMCID: PMC11482608DOI1 citations
With Mildred Unti · Pharmacology (PhD) · Class of 2024
RNA tertiary structure and conformational dynamics revealed by BASH MaP.
bioRxiv : the preprint server for biology · 2024
SRSamie R JaffreyMOMaxim Oleynikov
PMID: 38645201PMCID: PMC11030352DOI
With Maxim Oleynikov · Pharmacology (PhD)
Highly efficient cellular expression of circular mRNA enables prolonged protein expression.
Cell chemical biology · 2023
SRSamie R JaffreyMJMildred J Unti
PMID: 37883972PMCID: PMC10841545DOI60 citations
With Mildred Unti · Pharmacology (PhD) · Class of 2024
m⁶A governs length-dependent enrichment of mRNAs in stress granules.
Nature structural & molecular biology · 2023
SRSamie R JaffreyHXHui Xian Poh
PMID: 37710015PMCID: PMC10715973DOI48 citations
With Hui Xian Poh · Molecular Biology (PhD) · Class of 2024
Highly efficient cellular expression of circular mRNA enables prolonged protein expression.
bioRxiv : the preprint server for biology · 2023
SRSamie R JaffreyMJMildred J Unti
PMID: 37503010PMCID: PMC10369907DOI
With Mildred Unti · Pharmacology (PhD) · Class of 2024
BTG1 mutation yields supercompetitive B cells primed for malignant transformation.
Science (New York, N.Y.) · 2023
SRSamie R JaffreyHXHui Xian PohCMCoraline MlynarczykMTMatt Teater+13 more →AMAri M. Melnick
PMID: 36656933PMCID: PMC10515739DOI40 citations
With Hui Xian Poh · Molecular Biology (PhD) · Class of 2024
Alternative splicing of METTL3 explains apparently METTL3-independent m6A modifications in mRNA.
PLoS biology · 2022
SRSamie R JaffreyHXHui Xian PohAHAashiq H. Mirza
PMID: 35853000PMCID: PMC9295969DOI63 citations
With Hui Xian Poh · Molecular Biology (PhD) · Class of 2024
The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells.
Cancer discovery · 2020
SRSamie R JaffreyHXHui Xian Poh
PMID: 33023892PMCID: PMC8110214DOI338 citations
With Hui Xian Poh · Molecular Biology (PhD) · Class of 2024
Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells.
Angewandte Chemie (International ed. in English) · 2020
SRSamie R JaffreyJLJacob L LitkeHKHyaeyeong KimJWJiahui Wu
PMID: 31850609PMCID: PMC8158785DOI103 citations
With Jacob Litke · Tri-I Program in Chemical Biology (PhD) · Class of 2019
Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells.
Angewandte Chemie (International ed. in English) · 2020
SRSamie R JaffreyHKHyaeyeong KimJLJacob L LitkeJWJiahui Wu
PMID: 31850609PMCID: PMC8158785DOI103 citations
With Hyaeyeong Kim · Cell & Developmental Biology (PhD) · Class of 2020
A Fluorogenic RNA-Based Sensor Activated by Metabolite-Induced RNA Dimerization.
Cell chemical biology · 2019
SRSamie R JaffreyHKHyaeyeong Kim
PMID: 31631009PMCID: PMC6939632DOI47 citations
With Hyaeyeong Kim · Cell & Developmental Biology (PhD) · Class of 2020
Reading, writing and erasing mRNA methylation.
Nature reviews. Molecular cell biology · 2019
SRSamie R JaffreyRJRyan J RiesSZSara Zaccara
PMID: 31520073DOI2,182 citations
With Ryan Ries · Neuroscience (PhD) · Class of 2023
Live imaging of mRNA using RNA-stabilized fluorogenic proteins.
Nature methods · 2019
SRSamie R JaffreyHKHyaeyeong KimJWJiahui WuSZSara Zaccara
PMID: 31471614PMCID: PMC6719798DOI105 citations
With Hyaeyeong Kim · Cell & Developmental Biology (PhD) · Class of 2020
m⁶A enhances the phase separation potential of mRNA.
Nature · 2019
SRSamie R JaffreyRJRyan J RiesSZSara ZaccaraAOAnthony Olarerin-GeorgeBFBrian F Pickering
PMID: 31292544PMCID: PMC6662915DOI619 citations
With Ryan Ries · Neuroscience (PhD) · Class of 2023
Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts.
Nature biotechnology · 2019
SRSamie R JaffreyJLJacob L Litke
PMID: 30962542PMCID: PMC6554452DOI296 citations
With Jacob Litke · Tri-I Program in Chemical Biology (PhD) · Class of 2019
Detection of Low-Abundance Metabolites in Live Cells Using an RNA Integrator.
Cell chemical biology · 2019
SRSamie R JaffreyJLJacob L Litke
PMID: 30773480PMCID: PMC6474789DOI40 citations
With Jacob Litke · Tri-I Program in Chemical Biology (PhD) · Class of 2019
Distinguishing RNA modifications from noise in epitranscriptome maps.
Nature chemical biology · 2018
SRSamie R JaffreyAVAnya V Grozhik
PMID: 29443978DOI87 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
Epitranscriptomics: Shrinking maps of RNA modifications.
Nature · 2017
SRSamie R JaffreyAVAnya V Grozhik
PMID: 29072301DOI26 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex.
Nature chemical biology · 2017
SRSamie R JaffreyHKHyaeyeong KimXLXing LiJDJared D Moon
PMID: 28945233PMCID: PMC5679246DOI232 citations
With Hyaeyeong Kim · Cell & Developmental Biology (PhD) · Class of 2020
The m⁶A pathway facilitates sex determination in Drosophila.
Nature communications · 2017
SRSamie R JaffreyAVAnya V GrozhikCLChing-Jung LinVDVladimir DespicECEric C Lai
PMID: 28675155PMCID: PMC5500889DOI167 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
Mapping m⁶A at Individual-Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP).
Methods in molecular biology (Clifton, N.J.) · 2017
SRSamie R JaffreyAVAnya V GrozhikAOAnthony O Olarerin-George
PMID: 28349454PMCID: PMC5562447DOI83 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
Reversible methylation of m⁶A_m in the 5' cap controls mRNA stability.
Nature · 2016
SRSamie R JaffreyAVAnya V GrozhikBFBrian F PickeringQCQiuying ChenSSSteven S Gross+1 more →
PMID: 28002401PMCID: PMC5513158DOI971 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells.
Methods in enzymology · 2016
SRSamie R JaffreyJLJ L Litke
PMID: 27241761PMCID: PMC5540731DOI23 citations
With Jacob Litke · Tri-I Program in Chemical Biology (PhD) · Class of 2019
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome.
Nature methods · 2015
SRSamie R JaffreyAVAnya V GrozhikAOAnthony O Olarerin-GeorgeCMCem Meydan CEChristopher E Mason
PMID: 26121403PMCID: PMC4487409DOI1,388 citations
With Anna Grozhik · Neuroscience (PhD) · Class of 2018
In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies.
Chemistry & biology · 2015
SRSamie R JaffreyCWChristina W Kam
PMID: 26000751PMCID: PMC4441765DOI148 citations
With Christina Kam · Molecular Biology (PhD) · Class of 2021
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch.
Proceedings of the National Academy of Sciences of the United States of America · 2015
SRSamie R JaffreyJLJacob L Litke
PMID: 25964329PMCID: PMC4450428DOI193 citations
With Jacob Litke · Tri-I Program in Chemical Biology (PhD) · Class of 2019

Postdoc mentee

A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins.
Nucleic acids research · 2026
SRSamie R JaffreyQHQian HouKSKi Sung Park AHAashiq H. Mirza MMMateo Martinez Roque+1 more →
PMID: 42531073PMCID: PMC13421773DOI
With Qian Hou · Tri-I Program in Chemical Biology · Class of 2024
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins.
Nucleic acids research · 2026
SRSamie R Jaffrey KSKi Sung Park AHAashiq H. MirzaQHQian HouMMMateo Martinez Roque+1 more →
PMID: 42531073PMCID: PMC13421773DOI
With Ki Sung Park · Postdoc mentee
A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins.
Nucleic acids research · 2026
SRSamie R Jaffrey MMMateo Martinez Roque KSKi Sung Park AHAashiq H. MirzaQHQian Hou+1 more →
PMID: 42531073PMCID: PMC13421773DOI
With Mateo Martinez Roque · Postdoc mentee
Transcription Start Site Choice Regulates m⁶A Stoichiometry in Cap-Proximal Regions.
Genes · 2026
SRSamie R Jaffrey JLJianheng Liu
PMID: 42353811PMCID: PMC13298977DOI
With Jianheng Liu · Postdoc mentee
FTO depletion does not alter m⁶A stoichiometry in AML mRNA: a reassessment using direct RNA nanopore sequencing.
bioRxiv : the preprint server for biology · 2025
SRSamie R Jaffrey JLJianheng Liu
PMID: 41279954PMCID: PMC12633362DOI
With Jianheng Liu · Postdoc mentee
Establishing benchmarks for quantitative mapping of m ⁶ A by Nanopore Direct RNA Sequencing.
bioRxiv : the preprint server for biology · 2025
SRSamie R Jaffrey JLJianheng Liu
PMID: 41278928PMCID: PMC12636606DOI
With Jianheng Liu · Postdoc mentee
A portable poison exon for small-molecule control of mammalian gene expression.
Nature methods · 2025
SRSamie R JaffreyQHQian HouMOMaxim OleynikovXAXiaohan Alex MeiLDLinghao Dong+1 more →
PMID: 41184552PMCID: PMC13102273DOI2 citations
With Qian Hou · Tri-I Program in Chemical Biology · Class of 2024
A portable poison exon for small-molecule control of mammalian gene expression.
Nature methods · 2025
SRSamie R JaffreyTHTimo HagenQHQian HouMOMaxim OleynikovXAXiaohan Alex Mei+1 more →
PMID: 41184552PMCID: PMC13102273DOI2 citations
With Timo Hagen · Postdoc mentee
A portable poison exon for small-molecule control of mammalian gene expression.
Nature methods · 2025
SRSamie R Jaffrey XAXiaohan Alex MeiQHQian HouMOMaxim OleynikovLDLinghao Dong+1 more →
PMID: 41184552PMCID: PMC13102273DOI2 citations
With Xiaohan Alex Mei · Postdoc mentee
m⁶A alters ribosome dynamics to initiate mRNA degradation.
Cell · 2025
SRSamie R Jaffrey JLJianheng LiuSMShino MurakamiAOAnthony O Olarerin-GeorgeSZSara Zaccara+1 more →
PMID: 40328256PMCID: PMC12255529DOI36 citations
With Jianheng Liu · Postdoc mentee
m⁶A alters ribosome dynamics to initiate mRNA degradation.
Cell · 2025
SRSamie R JaffreyBHBen HawleySMShino MurakamiAOAnthony O Olarerin-GeorgeJLJianheng Liu+1 more →
PMID: 40328256PMCID: PMC12255529DOI36 citations
With Ben Hawley · Postdoc mentee
m⁶A alters ribosome dynamics to initiate mRNA degradation.
Cell · 2025
SRSamie R JaffreySZSara ZaccaraSMShino MurakamiAOAnthony O Olarerin-GeorgeJLJianheng Liu+1 more →
PMID: 40328256PMCID: PMC12255529DOI36 citations
With Sara Zaccara · Postdoc mentee
Decoding m⁶Am by simultaneous transcription-start mapping and methylation quantification.
eLife · 2025
SRSamie R Jaffrey JLJianheng LiuBRBen R Hawley
PMID: 40162895PMCID: PMC11957539DOI
With Jianheng Liu · Postdoc mentee
Decoding m⁶Am by simultaneous transcription-start mapping and methylation quantification.
eLife · 2025
SRSamie R JaffreyBRBen R HawleyJLJianheng Liu
PMID: 40162895PMCID: PMC11957539DOI
With Ben Hawley · Postdoc mentee
The pseudorabies virus UL13 protein kinase triggers phosphorylation of the RNA demethylase FTO, which is associated with FTO-dependent suppression of interferon-stimulated gene expression.
Journal of virology · 2025
SRSamie R Jaffrey JLJianheng Liu
PMID: 39791911PMCID: PMC11852732DOI10 citations
With Jianheng Liu · Postdoc mentee
Decoding m⁶Am by simultaneous transcription-start mapping and methylation quantification.
bioRxiv : the preprint server for biology · 2025
SRSamie R Jaffrey JLJianheng LiuBRBen R Hawley
PMID: 39677659PMCID: PMC11642800DOI
With Jianheng Liu · Postdoc mentee
Decoding m⁶Am by simultaneous transcription-start mapping and methylation quantification.
bioRxiv : the preprint server for biology · 2025
SRSamie R JaffreyBRBen R HawleyJLJianheng Liu
PMID: 39677659PMCID: PMC11642800DOI
With Ben Hawley · Postdoc mentee
Dinoflagellate mRNA is pervasively modified with m¹A.
EMBO reports · 2024
SRSamie R Jaffrey JLJianheng Liu
PMID: 39304776PMCID: PMC11549392DOI
With Jianheng Liu · Postdoc mentee
Engineering acyclovir-induced RNA nanodevices for reversible and tunable control of aptamer function.
Cell chemical biology · 2024
SRSamie R JaffreyQHQian HouTHTimo Hagen
PMID: 39191249PMCID: PMC11680490DOI4 citations
With Qian Hou · Tri-I Program in Chemical Biology · Class of 2024
Engineering acyclovir-induced RNA nanodevices for reversible and tunable control of aptamer function.
Cell chemical biology · 2024
SRSamie R JaffreyTHTimo HagenQHQian Hou
PMID: 39191249PMCID: PMC11680490DOI4 citations
With Timo Hagen · Postdoc mentee
Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells.
RNA biology · 2023
SRSamie R JaffreyQHQian Hou
PMID: 37129556PMCID: PMC10155629DOI15 citations
With Qian Hou · Tri-I Program in Chemical Biology · Class of 2024
mRNA ageing shapes the Cap2 methylome in mammalian mRNA.
Nature · 2023
SRSamie R JaffreyVDVladimir Despic
PMID: 36725932PMCID: PMC9891201DOI73 citations
With Vladimir Despic · Postdoc mentee
YTHDC2 control of gametogenesis requires helicase activity but not m⁶A binding.
Genes & development · 2022
SRSamie R JaffreyBRBen R HawleyCDChristopher D LimaSKScott Keeney
PMID: 35058317PMCID: PMC8887132DOI40 citations
With Ben Hawley · Postdoc mentee
Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors.
Cell chemical biology · 2021
SRSamie R JaffreySKSourav K DeyJDJared D MoonJWJiahui Wu
PMID: 34010626PMCID: PMC8573057DOI24 citations
With Sourav Dey · Postdoc mentee
Imaging Intracellular S-Adenosyl Methionine Dynamics in Live Mammalian Cells with a Genetically Encoded Red Fluorescent RNA-Based Sensor.
Journal of the American Chemical Society · 2020
SRSamie R JaffreySKSourav Kumar DeySRScott R Suter
PMID: 32698574PMCID: PMC8158784DOI66 citations
With Sourav Dey · Postdoc mentee
A Unified Model for the Function of YTHDF Proteins in Regulating m⁶A-Modified mRNA.
Cell · 2020
SRSamie R JaffreySZSara Zaccara
PMID: 32492408PMCID: PMC7508256DOI671 citations
With Sara Zaccara · Postdoc mentee
Reading, writing and erasing mRNA methylation.
Nature reviews. Molecular cell biology · 2019
SRSamie R JaffreySZSara ZaccaraRJRyan J Ries
PMID: 31520073DOI2,182 citations
With Sara Zaccara · Postdoc mentee
Live imaging of mRNA using RNA-stabilized fluorogenic proteins.
Nature methods · 2019
SRSamie R JaffreySZSara ZaccaraJWJiahui WuHKHyaeyeong Kim
PMID: 31471614PMCID: PMC6719798DOI105 citations
With Sara Zaccara · Postdoc mentee
RIBOTACs: Small Molecules Target RNA for Degradation.
Cell chemical biology · 2019
SRSamie R JaffreySKSourav K Dey
PMID: 31419417DOI72 citations
With Sourav Dey · Postdoc mentee
The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.
Nucleic acids research · 2019
SRSamie R JaffreyBRBen R Hawley
PMID: 31328227PMCID: PMC6735865DOI455 citations
With Ben Hawley · Postdoc mentee
m⁶A enhances the phase separation potential of mRNA.
Nature · 2019
SRSamie R JaffreySZSara ZaccaraRJRyan J RiesAOAnthony Olarerin-GeorgeBFBrian F Pickering
PMID: 31292544PMCID: PMC6662915DOI619 citations
With Sara Zaccara · Postdoc mentee
Identification of the m⁶Am Methyltransferase PCIF1 Reveals the Location and Functions of m⁶Am in the Transcriptome.
Molecular cell · 2019
SRSamie R JaffreyBRBen R HawleySZSara Zaccara
PMID: 31279658PMCID: PMC6703822DOI223 citations
With Ben Hawley · Postdoc mentee
Identification of the m⁶Am Methyltransferase PCIF1 Reveals the Location and Functions of m⁶Am in the Transcriptome.
Molecular cell · 2019
SRSamie R JaffreySZSara ZaccaraBRBen R Hawley
PMID: 31279658PMCID: PMC6703822DOI223 citations
With Sara Zaccara · Postdoc mentee
Transcriptome-Wide Mapping of m⁶ A and m⁶ Am at Single-Nucleotide Resolution Using miCLIP.
Current protocols in molecular biology · 2019
SRSamie R JaffreyBRBen R Hawley
PMID: 30874375PMCID: PMC6422687DOI28 citations
With Ben Hawley · Postdoc mentee
FTO controls reversible m⁶Am RNA methylation during snRNA biogenesis.
Nature chemical biology · 2019
SRSamie R JaffreyBRBen R HawleyVDVladimir DespicSSSteven S Gross
PMID: 30778204PMCID: PMC6984009DOI246 citations
With Ben Hawley · Postdoc mentee
FTO controls reversible m⁶Am RNA methylation during snRNA biogenesis.
Nature chemical biology · 2019
SRSamie R JaffreyVDVladimir DespicBRBen R HawleySSSteven S Gross
PMID: 30778204PMCID: PMC6984009DOI246 citations
With Vladimir Despic · Postdoc mentee
The N⁶-methyladenosine (m⁶A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells.
Nature medicine · 2017
SRSamie R JaffreySZSara ZaccaraBFBrian F PickeringMMMatthew MacKay+4 more →MGMichael G Kharas
PMID: 28920958PMCID: PMC5677536DOI1,090 citations
With Sara Zaccara · Postdoc mentee
The m⁶A pathway facilitates sex determination in Drosophila.
Nature communications · 2017
SRSamie R JaffreyVDVladimir DespicAVAnya V GrozhikCLChing-Jung LinECEric C Lai
PMID: 28675155PMCID: PMC5500889DOI167 citations
With Vladimir Despic · Postdoc mentee