Publications by authors named "Jeff Nivala"

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Structure-informed models for ionic current prediction in nanopore sequencing of expanded dna alphabets.
Ashley Stephenson, Jayson Sumabat, Hinako Kawabe, Sidharth Lakshmanan, Hyo Joong Kim, Jeff Nivala

Nucleic Acids Res· November 2025

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Hybridization-encoded DNA tags with paper-based readout for anti-forgery raw material tracking.
Jiaming Li, Alex Crown, Peter Ney, Sergey Yekhanin, Aditi Partap, Jeff Nivala

Nat Commun· July 2025

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Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design.
Carina Imburgia, Lee Organick, Karen Zhang, Nicolas Cardozo, Jeff McBride, Jeff Nivala

Nat Commun· July 2025

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Harnessing DNA computing and nanopore decoding for practical applications: from informatics to microRNA-targeting diagnostics.
Sotaro Takiguchi, Nanami Takeuchi, Vasily Shenshin, Guillaume Gines, Anthony J Genot, Jeff Nivala

Chem Soc Rev· January 2025

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'Do-it-yourself' data storage on DNA paves way to simple archiving system.
Carina Imburgia, Jeff Nivala

Nature· October 2024

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Multi-pass, single-molecule nanopore reading of long protein strands.
Keisuke Motone, Daphne Kontogiorgos-Heintz, Jasmine Wee, Kyoko Kurihara, Sangbeom Yang, Jeff Nivala

Nature· September 2024

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Data hazards in synthetic biology.
Natalie R Zelenka, Nina Di Cara, Kieren Sharma, Seeralan Sarvaharman, Jasdeep S Ghataora, Jeff Nivala

Synth Biol (Oxf)· June 2024

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De novo design of high-affinity binders of bioactive helical peptides.
Susana Vázquez Torres, Philip J Y Leung, Preetham Venkatesh, Isaac D Lutz, Fabian Hink, Jeff Nivala

Nature· February 2024

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Barcoding biomarkers with nanopore sequencing.
Ashley Stephenson, Jeff Nivala

Nat Nanotechnol· December 2023

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Physical Laboratory Automation in Synthetic Biology.
Ashley Stephenson, Lauren Lastra, Bichlien Nguyen, Yuan-Jyue Chen, Jeff Nivala

ACS Synth Biol· November 2023

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Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity.
Keisuke Motone, Daphne Kontogiorgos-Heintz, Jasmine Wee, Kyoko Kurihara, Sangbeom Yang, Jeff Nivala

bioRxiv· October 2023

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Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons.
Adam Kuzdraliński, Marek Miśkiewicz, Hubert Szczerba, Wojciech Mazurczyk, Jeff Nivala

Nat Commun· September 2023

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Design of stimulus-responsive two-state hinge proteins.
Florian Praetorius, Philip J Y Leung, Maxx H Tessmer, Adam Broerman, Cullen Demakis, Jeff Nivala

Science· August 2023

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Not if but when nanopore protein sequencing meets single-cell proteomics.
Keisuke Motone, Jeff Nivala

Nat Methods· March 2023

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Recording gene expression order in DNA by CRISPR addition of retron barcodes.
Santi Bhattarai-Kline, Sierra K Lear, Chloe B Fishman, Santiago C Lopez, Elana R Lockshin, Jeff Nivala

Nature· August 2022

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A nanopore interface for higher bandwidth DNA computing.
Karen Zhang, Yuan-Jyue Chen, Delaney Wilde, Kathryn Doroschak, Karin Strauss, Jeff Nivala

Nat Commun· August 2022

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Multiplexed direct detection of barcoded protein reporters on a nanopore array.
Nicolas Cardozo, Karen Zhang, Kathryn Doroschak, Aerilynn Nguyen, Zoheb Siddiqui, Jeff Nivala

Nat Biotechnol· January 2022

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Synthetic DNA applications in information technology.
Linda C Meiser, Bichlien H Nguyen, Yuan-Jyue Chen, Jeff Nivala, Karin Strauss

Nat Commun· January 2022

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Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis.
Keisuke Motone, Nicolas Cardozo, Jeff Nivala

iScience· September 2021

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Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP.
Jeff Nivala, Logan Mulroney, Qing Luan, Robin Abu-Shumays, Mark Akeson

Methods Mol Biol· March 2021

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Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases.
Mirkó Palla, Sukanya Punthambaker, Benjamin Stranges, Frederic Vigneault, Jeff Nivala

ACS Nano· January 2021

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Rapid and robust assembly and decoding of molecular tags with DNA-based nanopore signatures.
Kathryn Doroschak, Karen Zhang, Melissa Queen, Aishwarya Mandyam, Karin Strauss, Jeff Nivala

Nat Commun· November 2020

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Follow the barcoded microbes.
Jeff Nivala

Science· June 2020

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Molecular digital data storage using DNA.
Luis Ceze, Jeff Nivala, Karin Strauss

Nat Rev Genet· August 2019

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Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration.
Jeff Nivala, Seth L Shipman, George M Church

Nat Microbiol· March 2018

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