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Peer-Reviewed Journal Publications:

"Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer", O. K. Zahid, F. Rivas, F. Wang, K. Sethi, K. Reiss, S. Bearden, A. R. Hall, Nanomedicine: Nanotechnology, Biology and Medicine, 2021, PDF

"Direct detection of conserved viral sequences and other nucleic acid motifs with solid-state nanopores", K. Sethi, G. Dailey, O. K. Zahid, E. W. Taylor, J. Ruzicka, A. R. Hall, ACS Nano, 2021, PDF (Supplemental Information)

"Modular affinity-labeling of the cytosine demethylation base elements in DNA", F. Wang, O. K. Zahid, U. Ghanty , R. M. Kohli, A. R. Hall, Scientific Reports, 2020, PDF (Supplementary Information)

"Ovarian stiffness increases with age in the mammalian ovary and depends on collagen and hyaluronan matrices", F. Amargant, S. Manuel, Q. Tu, W. Parkes, F. Rivas, L. Zhou, J. Rowley, C. Villanueva, J. Hornick, G. Shekhawat, J. Wei, M. E. Pavone, A. R. Hall, M. Pritchard, F. Duncan, Aging Cell, 2020, PDF

"Mechanical Properties of Electrospun, Blended Fibrinogen: PCL Nanofibers", J. M. Sharpe, H. Lee, A. R. Hall, K. Bonin, M. Guthold, Nanomaterials, 10, 1843, 2020, PDF

"Drug compound screening in single and integrated multi-organoid body-on-a-chip systems", A. Skardal, J. Aleman, S. Forsythe, S. A. P. Rajan, S. Murphy, M. Devarasetty, Z. Pourhabibi Zarandi, G. Nzou, R. Wicks, H. Sadri-Ardekani, C. Bishop, S. Soker, A. R. Hall, T. Shupe, A. Atala, Biofabrication, 12, 025017, 2020  PDF


"Probing prodrug metabolism and reciprocal toxicity with an integrated and humanized multi-tissue organ-on-a-chip platform", S. A. P. Rajan, J. Aleman, M. Wan, N. Pourhabibi Zarandi, G. Nzou, S. Murphy, C. E. Bishop, H. Sadri-Ardekani, T. Shupe, A. Atala, A. R. Hall, A. Skardal, Acta Biomaterialia, 106,124-135, 2020 PDF

"Multi-domain photopatterned 3D tumor constructs in a micro-physiological system for analysis, quantification, and isolation of infiltrating cells", S. A. P. Rajan, A. Skardal, A. R. Hall, Advanced Biosystems, 4 (4), 1900273, 2020  PDF (Supplemental Information)

"Design of an Adhesive Film-Based Microfluidic Device for Alginate Hydrogel-Based Cell Encapsulation" K. Enck, S. A. P. Rajan, J. Aleman, S. Castagno, E. Long, F. Khalil, A. R. Hall, E. C. Opara, Annals of Biomedical Engineering, 48 (3), 1103–11, 2020 PDF

"Self-regenerating giant hyaluronan polymer brushes", W. Wei, J. L. Faubel, H. Selvakumar, D. T. Kovari, J. Tsao, F. Rivas, A. T. Mohabir, M. Krecker, E. Rahbar, A. R. Hall, M. A. Filler, J. L. Washburn, P. H. Weigel, J. E. Curtis, Nature Communications, 10, 5527, 2019 PDF

"Simple and efficient room-temperature release of biotinylated nucleic acids from streptavidin and its application to selective molecular detection", S. Bearden, F. Wang, A. R. Hall, Analytical Chemistry, 91 (13), 7996-8001, 2019 PDF (Supplemental Information)

“Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores”, L. J. de Vreede, C. Ying, J. Houghtaling, J. F. Da Silva, A. R. Hall, A. Lovera, M. Mayer, Nanotechnology, 30 (26), 265301, 2019 PDF


"Estimation of shape, volume, and dipole moment of individual proteins freely transiting a synthetic nanopore", J. Houghtaling, C. Ying, O. M. Eggenberger, A. Fennouri, S. Nandivada, M. Acharjee, J. Li, A. R. Hall, M. Mayer, ACS Nano, 13 (5), 5231–5242, 2019  PDF


"Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers", O. M Eggenberger, G. Leriche, T. Koyanagi, C. Ying, J. Houghtaling, T. B. H. Schroeder, J. Yang, J. Li, A. Hall, M. Mayer, Nanotechnology, 30 (32), 325504, 2019 PDF

"Label-free analysis of physiological hyaluronan size distribution with a solid-state nanopore sensor", F. Rivas, O. K. Zahid, H. L. Reesink, B. T. Peal, A. J. Nixon, P. L. DeAngelis, A. Skardal, E. Rahbar, and A. R. Hall, Nature Communications, 9, 1037, 2018 PDF (Supplemental Information) (Press)

"In vitro patient-derived 3D mesothelioma tumor organoids facilitate patient-centric therapeutic screening", A. R. Mazzocchi AR, S. A. P. Rajan, K. I. Votanopoulos, A. R. Hall, A. Skardal, Scientific Reports, 8, 2886, 2018 PDF

"Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process", F. Wang, O. K. Zahid, B. Swain, D. Parsonage, T. Hollis, S. Harvey, F. Perrino, R. M. Kohli, E. W. Taylor, A. R. Hall, Nano Letters, 17 (11), 7110–7116, 2017 PDF (Supplemental Information)

"Multi-tissue interactions in an integrated three-tissue organ-on-a-chip platform", A. Skardal, S. Murphy, M. Devarasetty, I. Mead, H.-W. Kang, Y.-J. Seol, Y. S. Zhang, S. R. Shin, L. Zhao, J. Aleman, A. R. Hall, T. Shupe, A. Kleensang, M. Dokmeci, S. J. Lee, J. Jackson, J. Yoo, T. Hartung, A. Khademhosseini, S. Soker, C. Bishop, A. Atala, Scientific Reports, 7, 8837, 2017 PDF (Press)

"Solid-state nanopore analysis of alcohol-soluble molecules", D. Basu Roy,  A. R. Hall, Analyst, 142, 1676-1681, 2017 PDF (Supplemental Information)

"Solid-state nanopore localization by controlled breakdown of selectively thinned membranes", A. T Carlsen, K. Briggs, A. R. Hall, V. Tabard-Cossa, Nanotechnology, 28 (8), 085304, 2017 PDF (Supplemental Information)

"Real-time shape approximation and fingerprinting of single proteins using a nanopore", E. C. Yusko, B. R. Bruhn, O. M. Eggenberger, J. Houghtaling, R. C. Rollings, N. C. Walsh, S. Nandivada, M. Pindrus, A. R. Hall, D. Sept, J. Li, D. S. Kalonia, M. Mayer, Nature Nanotechnology, 12 (4), 360-367, 2016 PDF (Supplemental Information)

"Differentiation of Specific Cancer Biomarkers with Solid-state Nanopores", W. Ali, M. U. Raza, M. A. I. Mahmood, P. B. Allen, A. R. Hall, Y. Wan, S. M. Iqbal, Functional Nanostructures, 2016 PDF

"Quantifying mammalian genomic DNA hydroxymethylcytosine content using solid-state nanopores", O. K. Zahid, B. S. Zhao, C. He, A. R. Hall, Scientific Reports, 6, 29565, 2016 PDF (Supplemental Information) (PRESS)

"Sequence-specific recognition of microRNAs and other short nucleic acids with solid-state nanopores", O. K. Zahid, F. Wang, J. A. Ruzicka, E. W. Taylor, A. R. Hall, Nano Letters, 16 (3), 2033–2039, 2016 PDF (Supplemental Information) (Press: 1, 2, 3, 4, 5, 6, 7, Audio)


"In situ patterned micro 3-D liver constructs for parallel toxicology testing in a fluidic device", A. Skardal, M. Devarasetty, S. Soker, A. R. Hall, Biofabrication, 7 (3), 031001, 2015 PDF (PRESS)


"Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA", M. M. Marshall, J. A. Ruzicka, O. K. Zahid, V. C. Henrich, E. W. Taylor, A. R. Hall, Langmuir, 31 (15), 4582–4588, 2015. PDF


"Controlled Translocation of DNA Through Nanopores in Carbon Nano-, Silicon-Nitride- and Lipid-Coated Membranes", A. Sischka, L. Galla, A. J. Meyer, A. Spiering, S. Knust, M. Mayer, A. R. Hall, A. Beyer, P. Reimann, A. Gölzhäuser, D. Anselmetti, Analyst, 140, 4843-4847, 2015. PDF


"Detecting DNA depurination with solid-state nanopores", M. M. Marshall, J. A. Ruzicka, E. W. Taylor, A. R. Hall, PLoS ONE, 9 (7), e101632, 2014 PDF (Press)


"Hydrodynamic slip on DNA observed by optical tweezers-controlled translocation experiments with solid-state and lipid-coated nanopores", L. Galla, A. Meyer, A. Spiering, A. Sischka, M. Mayer, A. R. Hall, P. Reimann, D. Anselmetti, Nano Letters, 14 (7), 4176–4182,  2014 PDF


"Selective detection and quantification of modified DNA with solid-state nanopores", A. T. Carlsen, O. K. Zahid, J. A. Ruzicka, E. W. Taylor, A. R. Hall, Nano Letters, 14 (10), 5488-92, 2014 PDF (Supplementary Information)

(Cover article)


"Solid-state nanopores and nanopore arrays optimized for optical detection", F. Sawafta, B. Clancy, A. T. Carlsen, M. Huber, A. R. Hall, Nanoscale, 6, 6991-6996, 2014 PDF (Supplementary Information) (Press)


"Membrane thickness dependence of nanopore formation with a focused Helium ion beam", F. Sawafta, A. T. Carlsen, A. R. Hall, Sensors, 14 (5), 8150-61, 2014 PDF (Featured in the Special Issue: "Nanopore Sensors: Fabrications, Properties, and Applications")


"Interpreting the conductance blockades of DNA translocations through solid-state nanopores", A. T. Carlsen, O. K. Zahid, J. A. Ruzicka, E. W. Taylor, A. R. Hall, ACS Nano, 8 (5), 4754–4760, 2014 PDF (Supplementary Information)


"Nanotechnology in Biological Detection and Characterization", E. D. Goluch, A. R. Hall, NanoLIFE, 3 (1), 1302001, 2013 PDF


"In Situ Thickness Assessment During Ion Milling of a Free-Standing Membrane Using Transmission Helium Ion Microscopy", A. R. Hall, Microscopy and Microanalysis, 19 (3), 740-744, 2013 PDF (Zeiss Application Note here)

"Direct- and Transmission-milling of Suspended Silicon Nitride Membranes with a Focused Helium Beam", M. M. Marshall, J. Yang, A. R. Hall, Scanning, 34 (2), 101-106, 2012 PDF

"Rapid and Precise Scanning Helium Microscope Milling of Solid-state Nanopores for Biomolecule Detection", J. Yang, D. C. Ferranti, L. A. Stern, C. A. Sanford, J. Huang, Z. Ren, L.-C. Qin, A. R. Hall, Nanotechnology, 22 (28), 285310, 2011 PDF (Zeiss Application Note here)

"Translocation of Single-Wall Carbon Nanotubes Through Solid-State Nanopores", A. R. Hall,  J. M. Keegstra, M. C. Duch, M. C. Hersam, C. Dekker, Nano Letters, 11 (6), 2446, 2011 PDF

"Highly Controllable Near-Surface Swimming of Magnetic Janus Nanorods: Application to Payload Capture and Manipulation", L. O. Mair, B. A. Evans, A. R. Hall, J. Carpenter, A. R. Shields, M. Millard, K. Ford, R. Superfine, J. Phys. D: Appl. Phys., 44 (12), 125001, 2011 PDF

"Hybrid Pore Formation by Directed Insertion of Alpha-haemolysin into Solid-state Nanopores", A. R. Hall, A. Scott, D. Rotem, K. Metah, H. Bayley, C. Dekker, Nature Nanotechnology, 5 (12), 874-7, 2010 PDF (Supplementary Information) (Press: 1  2  3  4  5  6

“Controlling Nanopore Size, Shape and Stability”, M. van den Hout, A. R. Hall, M. Y. Wu, H. W. Zanbergen, C. Dekker, N. H. Dekker, Nanotechnology, 21 (11), 115304, 2010 PDF (Supplementary Information)

“Detection of Local Protein Structures Along DNA Using Solid-State Nanopores”, S. Kowalczyk, A. R. Hall, C. Dekker, Nano Letters, 10 (1), 324-8, 2010 PDF (Supplementary Information)

“Electrophoretic Force on a Protein-Coated DNA Molecule in a Solid-State Nanopore”, A. R. Hall, S. van Dorp, S. G. Lemay, C. Dekker, Nano Letters, 9 (12), 4441-5, 2009 PDF (Supplementary Information) (Press)

“Translocation of RecA-Coated dsDNA through Solid-State Nanopores”, R. M. M. Smeets, S. Kowalczyk, A. R. Hall, N. H. Dekker, C. Dekker, Nano Letters, 9 (9), 3089-95, 2009 PDF (Cover article)

“A Self-Sensing Nanomechanical Resonator Built on a Single-Walled Carbon Nanotube”, A. R. Hall, M. R. Falvo, R. Superfine, S. Washburn, Nano Letters, 8 (11), 3726-9, 2008 PDF

“Electromechanical Response of Single-Wall Carbon Nanotubes to Torsional Strain in a Self-Contained Device”, A. R. Hall, M. R. Falvo, R. Superfine, S. Washburn, Nature Nanotechnology, 2 (7), 413-6, 2007 PDF (Supplementary Video)

“Experimental Measurement of Single-wall Carbon Nanotube Torsional Properties”, A. R. Hall, L. An, J. Liu, L. Vicci, M. R. Falvo, R. Superfine, S. Washburn, Phys. Rev. Lett., 96, 256102, 2006 PDF (Correction published Aug. 2010)

“Resonant Oscillators with Carbon-Nanotube Torsion Springs”, S. J. Papadakis, A. R. Hall, P. A. Williams, L. Vicci, M. R. Falvo, R. Superfine, S. Washburn, Phys. Rev. Lett., 93, 146101, 2004 PDF

“A Simple and Efficient Method for Carbon Nanotube Attachment to Scanning Probes and Other Materials”, A. Hall, W.G. Matthews, M.R. Falvo, R. Superfine, S. Washburn, Appl. Phys. Lett., 82 (15), 2506-8, 2003 PDF

Review Articles:

“Torsional electromechanical systems based on carbon nanotubes”, A. R. Hall, S. A.  Paulson, T. Cui, J. P. Lu, L.-C. Qin, S. Washburn, Reports on Progress in Physics, 75, 116501, 2012 PDF (Cover article)

"Solid-state nanopores: From fabrication to application", A .R. Hall, Microscopy Today, 20 (5), 24-29, 2012 PDF

Book Chapters:

"Microfluidics in cell and tissue studies", S.A.P. Rajan, P. Hambright, R.C. Burke, A.R. Hall, in Tumor Organoids, (Ed. S. Soker, A. Skardal), Springer Press, 2016 PDF

"Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis", O.K. Zahid and A.R. Hall, in Helium Ion Microscopy, (Ed. G. Hlawacek, A. Gölzhäuser), Springer Press, 2016 PDF

"Characterization of Biological and Condensed Matter at the Nanoscale", A.R. Hall, O.K. Zahid, F. Sawafta, A.T. Carlsen, in Advances in Nanoscience and Nanoengineering, (Ed. A.D. Kelkar, D. Herr, J.G. Ryan), CRC Press, 2013 PDF

"Measuring Single-Wall Carbon Nanotubes with Solid-State Nanopores", A .R. Hall, J.M. Keegstra, M.C. Duch, M.C. Hersam, C. Dekker, in Nanopore-based technology: single molecule characterization and DNA sequencing, (Ed. M. Gracheva,; Humana Press, 2011) Vol. “Nanopore Sequencing technology”, Series ‘Methods in Molecular biology ‘ (series editor J.M. Walker) PDF

"Molecular Detection and Force Spectroscopy in Solid-State Nanopores with Integrated Optical Tweezers", A .R. Hall and C. Dekker, in Nanopores: Sensing Fundamental Biological Interactions at the Single Molecule Level (Eds. R. Bashir, S. Iqbal; Springer, 2011) PDF



"Development and Application of a Modular Enzymatic Labeling Process for the Analysis of Diverse DNA Base Modifications", F. Wang, 2021, PDF

"Integrating Advanced 3D Cell Culture Techniques with Rapid-Prototyping Microfluidics for Translational Applications", S. A. P. Rajan, 2019, PDF

"Detection of Nucleic Acid Disease Biomarkers using Solid-State Nanopores", O. K. Zahid, 2017, PDF

"Solid-State Nanopores: A New Platform for DNA Biomarker Discovery", M. M. Marshall, 2014 PDF


"Material and Device Investigations on a Carbon Nanotube-Based Torsional Nanoelectromechanical System", A. R. Hall, 2007 PDF