Publications

“Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology.”

Maharjan S, Gamper H, Yamaki Y, Christian T, Henley RY, Li N, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou Y
Nature Communications, 15 , 9008 (2024).

“Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls.”

Makhamreh A, Tavakoli S, Fallahi A, Kang X, Gamper H, Nabizadehmashhadtoroghi M, Jain M, Hou Y, Rouhanifard S, Wanunu M
Scientific Reports, 14 , 22457 (2024).

“Hydrophilicity and surface charge modulation of Ti3C2Tx MXene based membranes for water desalination.”

Pandey L, Liang W, VahidMohammadi A, Zhang T, Gogotsi Y, Wanunu M
RSC Advances, 14, 21635-21643 (2024).

“Electro-osmotic flow generation via a sticky ion action.”

Mehrafrooz B, Yu L, Pandey L, Siwy ZS, Wanunu M, Aksimentiev A
ACS Nano, 18, 17521-17533 (2024).

“A Marcus-type inverted region in the translocation kinetics of a knotted protein.”

Tripathi P, Mehrafrooz B, Aksimentiev A, Jackson SE, Gruebele M, Wanunu M
Journal of Physical Chemistry Letters, 14, 47, 10719–10726(2023).

“Nanopore-Based Fingerprint Immunoassay Based on Rolling Circle Amplification and DNA Fragmentation.”

Kang X, Wu C, Alibakhshi MA, Liu X, Yu L, Walt DR, Wanunu M
ACS Nano, 6, 5412–5420 (2023).

“Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing.”

Tavakoli S, Nabizadeh M, Makhamreh A, Gamper H, McCormick CA, Rezapour NK, Hou Y, Wanunu M, Rouhanifard S
Nature Communications 14, 334(2023).

“Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore.”

Yu L, Kang X, Li F, Mehrafrooz B, Makhamreh A, Fallahi A, Foster JC, Aksimentiev A, Chen M, Wanunu M.
Nature Biotechnology, 41, 1130–1139 (2023).

“Scaled-up Synthesis of Freestanding Molybdenum Disulfide Membranes for Nanopore Sensing.”

Alibakhshi MA, Kang X, Clymer D, Zhang Z, Vargas A, Meunier V, Wanunu M.
Advanced Materials, 35,  2207089 (2022).

“High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized Within a Solid-State Nanopore.”

Mojtabavi M, Greive S, Antson A, Wanunu M.
Journal of the American Chemical Society  144, 49, 22540–22548 (2022).

“Threading single proteins through pores to compare their energy landscapes.”

Tripathi P, Firouzbakht A, Gruebele M, Wanunu M.
Proceedings of the National Academy of Sciences of USA, 119 (39) e2202779119 (2022).

“Direct Observation of Single-Protein Transition State Passage by Nanopore Ionic Current Jumps.”

Tripathi P, Firouzbakht A, Gruebele M, Wanunu M.
Journal of Physical Chemistry Letters  13, 5918–5924 (2022).

“Discrimination of RNA fiber structures using solid-state nanopores.”

Tripathi P, Chandler M, Maffeo CM, Fallahi A, Makhamreh A, Halman J, Aksimentiev A, Afonin KA, Wanunu M.
Nanoscale , D1NR08002D (2022).

“Control of subunit stoichiometry in single-chain MspA nanopores.”

Pavlenok M, Yu L, Herrmann D, Wanunu M, Niederweis M
Biophysical Journal 121, 1–13 (2022).

“Ionically Active MXene Nanopore Actuators.”

Mojtabavi M, Tsai W, VahidMohammadi A, Zhang T, Gogogtsi Y, Balke N, Wanunu M
Small, 2105857 (2022).

“Rapid Identification of DNA Fragments through Direct Sequencing with Electro-Optical Zero-Mode Waveguides.”

Farhangdoust F, Alibakhshi MA, Cheng F, Liang W, Liu Y, Wanunu M
Advanced Materials (2021).

“2D titanium and vanadium carbide MXene heterostructures for electrochemical energy storage.”

VahidMohammadi A, Liang W, Mojtabavi M, Wanunu M, Beidaghi M
Energy Storage Materials, 41, 554-562 (2021).

“Electrical unfolding of cytochrome c during translocation through a nanopore constriction.”

Tripathi P, Benabbas A, Mehrafrooz B, Yamazaki H, Aksimentiev A, Champion P, Wanunu M
Proceedings of the National Academy of Sciences of the USA, 118, 17 (2021).

“MoS2 Nanosheets with Narrowest Excitonic Line Widths Grown by Flow-Less Direct Heating of Bulk Powders: Implications for Sensing and Detection.”

“Stable Polymer Bilayers for Protein Channel Recordings at High Guanidinium Chloride Concentrations.”

Yu L, Kang X, Alibakhshi MA, Pavlenok M, Niederweis M, Wanunu M
Biophysical Journal, 120, 1-5 (2021).

“Wafer-Scale Lateral Self-Assembly of Mosaic Ti3C2Tx MXene Monolayer Films.”

Mojtabavi M, VahidMohammadi A, Ganeshan K, Hejazi D, Shahbazmohamadi S, Kar S, van Duin A, Wanunu M.
ACS Nano, 15, 625-636 (2021).

“High permeability sub-nanometre sieve composite MoS2 membranes.”

Sapkota B, Liang W, VahidMohammadi A, Karnik R, Noy A, Wanunu M
Nature Communications, 11, 2747 (2020).

“How Nanopore Translocation Experiments Can Measure RNA Unfolding.”

Bandarkar P, Yang H, Henley RY, Wanunu M, and Whitford PC
Biophysical Journal, 118, 1-9 (2020).

“Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors.”

Tripathi P, Shuai L, Joshi H, Yamazaki H, Fowle WH, Aksimentiev A, Fenniri H, and Wanunu M
Journal of the American Chemical Society, 142, 1680-1685 (2020).

“Strong Electroosmotic Coupling Dominates Ion Conductance of 1.5 nm Diameter Carbon Nanotube Porins.”

Yao YC, Taqieddin A, Alibakhshi MA, Wanunu M, Aluru N, and Noy A
ACS Nano 13, 12851-12859 (2019).

“One-Pot Species Release and Nanopore Detection in a Voltage-Stable Lipid Bilayer Platform.”

Kang X, Alibakhshi MA, and Wanunu M
Nano Letters 19, 9145-9153 (2019).

“Single-Molecule Sensing Using Nanopores in Two-Dimensional Transition Metal Carbide (MXene) Membranes.”

Mojtabavi M, VahidMohammadi A, Liang W, Beidaghi M, Wanunu M.
ACS Nano, 13, 3042-3053 (2019)

“Assembling 2D MXenes into Highly Stable Pseudocapacitive Electrodes with High Power and Energy Densities.”

VahidMohammadi A, Mojtabavi M, Caffrey NM, Wanunu M, and Beidaghi M
Advanced Materials 31, 1806931 (2019).

“Porous Zero-Mode Waveguides for Picogram-Level DNA Capture.”

Jadhav V, Hoogerheide D, Korlach J, and Wanunu M
Nano Letters, 19, 921-292 (2019).

“Abnormal Ionic-Current Rectification Caused by Reversed Electroosmotic Flow under Viscosity Gradients across Thin Nanopores.”

Qiu Y, Siwy Z, and Wanunu M
Analytical Chemistry, 91, 1996-1004 (2018).

“Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores.”

Yamazaki H, Hu R, Zhao Q, and Wanunu M
ACS Nano, 12, 12472-12481 (2018).

“Thermostable Virus Portal Proteins As Reprogrammable Adapters For Solid-State Nanopore Sensors.”

Cressiot B, Greive S, Mojtabavi M, Antson AA, and Wanunu M
Nat Comm, 9, 4652 (2018).

“Femtosecond Photonic Viral Inactivation Probed Using Solid-State Nanopores.”

Nazari M, Li X, Alibakhshi MA, Yang H, Souza K, Gillespie C, Gummuluru S, Hong MK, Reinhard BM, Korolev KS, Ziegler LD, Zhao Q, Wanunu M, and Erramilli S
Nano Futures, 2, 045005 (2018).

“Differential Enzyme Flexibility Probed Using Solid-State Nanopores.”

Hu R, Rodrigues JV, Waduge P, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, and Wanunu M
ACS Nano, 12, 4494-4502 (2018).

“Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization.”

Cressiot B, Greive SJ, Si W, Pascoa T, Mojtabavi M, Chechik M, Jenkins HT, Lu X, Zhang K, Aksimentiev A, Antson F, and Wanunu M
ACS Nano, 11, 11931–11945 (2017)

“Label-Free Single-Molecule Thermoscopy Using a Laser-Heated Nanopore.”

Yamazaki H, Hu R, Henley RY, Halman J, Afonin KA, Yu D, Zhao Q, and Wanunu M
Nano Letters, 17, 7067–7074 (2017)

“Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores.”

Alibakhshi MA, Halman JR, Wilson J, Aksimentiev A, Afonin KA, and Wanunu M
ACS Nano, 11, 9701–9710 (2017)

“Length-Independent DNA Packing into Nanopore Zero-Mode Waveguides for Low-Input DNA Sequencing.”

Larkin J, Henley RY, Jadhav V, Korlach J, and Wanunu M
Nature Nanotechnology, 12, 1169–1175 (2017)

“Enhanced water permeability and tunable ion selectivity in subnanometer carbon nanotube porins.”

Tunuguntla RH, Henley RY, Yao YC, Pham TA, Wanunu M, and Noy A
Science 357, 792-796 (2017)

“Driven translocation of a semi-flexible polymer through a nanopore.”

Sarabadani J, Ikonen T, Mokkonen H, Ala-Nissila T, Carson S, and Wanunu M
Scientific Reports, 7, 7423 (2017).

“Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes.”

Waduge P, Hu R, Bandarkar P, Yamazaki H, Cressiot B, Zhao Q, Whitford PC, and Wanunu M
ACS Nano, 11, 5706–5716 (2017).

“Peptide-Decorated Tunable-Fluorescence Graphene Quantum Dots.”

Sapkota B, Benabbas A, Lin HYG, Liang W, Champion P, and Wanunu M
ACS Applied Materials and Interfaces, 9, 9378–9387 (2017).

“Graphene Symmetry Amplified by Designed Peptide Self-Assembly.”

Mustata M, Kim YH, Zhang J, DeGrado WF, Grigoryan G, and Wanunu M
Biophysical Journal, 110, 2507–2516 (2016).

“Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity.”

Henley RY, Ashcroft BA, Farrell I, Cooperman BS, Lindsay S, and Wanunu M
Nano Letters, 16, 138–144 (2016).

“Distance-Dependent Energy Transfer Between CdSe/CdS Quantum Dots and A Two-Dimensional Semiconductor.”

Goodfellow KM, Chakraborty C, Sowers K, Waduge P, Wanunu M, Krauss T, Driscoll K, and Vamivakas AN
Applied Physics Letters, 108, 021101 (2016).

“Osmium-Based Pyrimidine Contrast Tags for Enhanced Nanopore-Based DNA Base Discrimination.”

Henley RY, Vazques-Pagan AG, Johnson M, Kanavarioti A, and Wanunu M
PLoS One, 0142155 (2015).

“Direct Analysis of Gene Synthesis Reactions Using Solid-State Nanopores.”

Carson S, Wick ST, Carr PA, Wanunu M, and Aguilar CA
ACS Nano, 9, 12417–12424 (2015).

“Hydroxymethyluracil Modifications Enhance The Flexibility and Hydrophilicity of Double-Stranded DNA.”

Carson S, Wilson J, Aksimentiev A, Weigele P, and Wanunu M
Nucleic Acids Research, ASAP (2015).

“Simultaneous Electro-Optical Tracking for Nanoparticle Recognition and Counting.”

Angeli E, Volpe A, Fanzio P, Repetto L, Firpo G, Guida P, Lo Savio R, Wanunu M, and Valbusa U
Nano Letters, 15, 5696–5701 (2015).

“Direct and Scalable Deposition of Atomically Thin Low-Noise MoS2 Membranes on Apertures.”

Waduge P, Bilgin I, Larkin J, Henley RY, Goodfellow K, Graham AC, Bell DC, Vamivakas N, Kar S, and Wanunu M
ACS Nano, 9, 7352–7359 (2015).

“Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability.”

Langecker M, Ivankin A, Carson S, Kinney SRM, Simmel F, and Wanunu M
Nano Letters, 15, 783–790 (2015).

“Programmed Synthesis of Freestanding Graphene Nanomembrane Arrays.”

Waduge P, Larkin J, Upmanyu M, Kar S, and Wanunu M
Small, 11, 597-603 (2015).

“Smooth DNA transport through a Narrowed Pore Geometry.”

Carson S, Wilson J, Aksimentiev A, and Wanunu M
Biophysical Journal, 107, 2381–2393 (2014).

“Label-Free Optical Detection of Biomolecular Translocation through Nanopore Arrays.”

Ivankin A*, Henley RY*, Larkin J, Carson S, Toscano M, and Wanunu M
ACS Nano, 10, 10774–10781 (2014).

“Reversible Positioning of Single Molecules inside Zero-Mode Waveguides.”

Larkin J, Foquet M, Turner SW, Korlach J, and Wanunu M
Nano Letters, 14, 6023–6029 (2014).

“Nanopore-Based Conformational Analysis of a Viral RNA Drug Target.”

Shasha C*, Henley RY*, Stoloff DH, Rynearson KD, Hermann T, and Wanunu M
ACS Nano, 8, 6425–6430 (2014).

“Graphene Nanopore Support System for Simultaneous High Resolution AFM Imaging and Conductance Measurements.”

Connelly L, Meckes B, Larkin J, Gillman AL, Wanunu M, and Lal R
ACS Applied Materials and Interfaces, 6, 5290-5296, (2014).

“High-Bandwidth Protein Analysis Using Solid-State Nanopores.”

Larkin J, Henley RY, Muthukumar M, Rosenstein JK, and Wanunu M
Biophysical Journal, 106(3), 696-704 (2014).

“Slow DNA Transport through Nanopores in Hafnium Oxide Membranes.”

Larkin J*, Henley R*, Bell DC, Cohen-Karni T, Rosenstein JK, and Wanunu M
ACS Nano, 7, 10121-10128 (2013).

“Fast, Label-Free Force Spectroscopy of Histone-DNA Interactions in Individual Nucleosomes Using Nanopores.”

Ivankin A, Carson S, Kinney SRM, and Wanunu M
Journal of the American Chemical Society, 135, 15350-15352 (2013).

“Nanocomposite Gold-Silk Nanofibers.”

Cohen-Karni T, Jeong KJ, Tsui J, Reznor G, Mustata M, Wanunu M, Graham A, Marks C, Bell DC, Langer R, Kohane DS
Nano Letters, 12, 5403-5406 (2012)