Publications

2025

Harnessing Dynamic Supramolecular Interactions for Lanthanide Detection via Computational Pattern Recognition of Magnetic Resonance Fingerprints

Goren E., Subramani B., Avram L., Falkovich A. H., Perlman O. & Bar-Shir A. (2025) Journal of the American Chemical Society. 147, 22, p. 18972-18981

Efficient Synthesis of Polymeric Fluorinated Nanoparticles with High Fluorine Content via Aqueous Photo-Polymerization-Induced Self-Assembly for 19F MRI Application

Chang Y., Ediriweera G. R., Xu W., Wang Q., Xu X., Zhang Y., Peng H., Liu K., Bar-Shir A., Whittaker A. K. & Fu C. (2025) ACS Nano. 19, 14, p. 14200-14212

In vivo 2H-MR spectroscopy and imaging of hepatic metabolic formation of trimethylamine-N-oxide

Dessau H., Harris T., de Graaf R. A., Montrazi E. T., Allouche-Arnon H. & Bar-Shir A. (2025) Magnetic Resonance in Medicine. 94, 2, p. 521-529

Hostguest geometry in paramagnetic cavitands elucidated by 19F electron-nuclear double resonance

Bogdanov A., Seal M., Goren E., Bar-Shir A. & Goldfarb D. (2025) Physical Chemistry Chemical Physics. 27, 7, p. 3885-3896

Voices of Nanomedicine: Blueprint Guidelines for Collaboration in Addressing Global Unmet Medical Needs

Prasad R., Ghosh A., Patel V., Peng B., Mendes B. B., Win E. H. A., Delogu L. G., Wong J. Y., Pischel K. J., Bellare J. R., Bar-Shir A., Thakor A. S., Parak W. J., Bhujwalla Z. M., Zhang Y. S., Kommineni N., Rotello V. M., Cai W., Lammers T., Odom T. W., Padmanaban G., Peer D., Lovell J. F., Srivastava R., Langer R. & Conde J. (2025) ACS Nano. 19, 3, p. 2979-2991

Deuterated Nanopolymers for Renal and Lymphatic Imaging via Quantitative Deuterium MRI

Fries L. M., Montrazi E. T., Allouche-Arnon H., Opazo F., Bar-Shir A., Frydman L. & Glöggler S. (2025) Nano Letters. 25, 5, p. 1758-1764

2024

A Reactive and Specific Sensor for Activity-Based 19F-MRI Sensing of Zn2+

Lee L. M., Tirukoti N. D., Subramani B., Goren E., Diskin-Posner Y., Allouche-Arnon H. & Bar-Shir A. (2024) ACS Sensors. 9, 11, p. 5770-5775

A Genetically Engineered Reporter System Designed for 2H-MRI Allows Quantitative In Vivo Mapping of Transgene Expression

Allouche-Arnon H., Montrazi E. T., Subramani B., Fisler M., Spigel I., Frydman L., Mehlman T., Brandis A., Harris T. & Bar-Shir A. (2024) Journal of the American Chemical Society. 146, 46, p. 31624-31632

Nanofluorides: Inorganic fluoride nanocrystals for 19F MRI

Cohen D., Mashiach R., Allouche-Arnon H. & Bar-Shir A. (2024) Fluorine Magnetic Resonance Imaging : Methods and Applications in Biomedicine . p. 33-59

Paramagnetic MgF2 Nanocrystals for 19F Magnetic Resonance Imaging

Cohen D., Brontvein O. & Bar-Shir A. (2024) ACS Applied Nano Materials. 7, 7, p. 6791-6796

Proteolytic Vesicles Derived from Salmonella enterica Serovar Typhimurium-Infected Macrophages: Enhancing MMP-9-Mediated Invasion and EV Accumulation

Nudelman A., Shenoy A., Allouche-Arnon H., Fisler M., Rosenhek-Goldian I., Dayan L., Abou Karam P., Porat Z., Solomonov I., Regev-Rudzki N., Bar-Shir A. & Sagi I. (2024) Biomedicines. 12, 2, 434.

2023

NMR exchange dynamics studies of metal-capped cyclodextrins reveal multiple populations of host-guest complexes in solution

Goren E., Iron M. A., Diskin-Posner Y., Falkovich A., Avram L. & Bar-Shir A. (2023) Chemical Science. 14, 41, p. 11351-11358

Cooperative Doping in Ultrasmall BaF2 Nanocrystals for Multimodal 19F-MRI and CT Applications

Cohen D., Houben L., Galisova A., Feldman Y., Fox S., Biton I. E. & Bar-Shir A. (2023) ACS Applied Nano Materials. 6, 14, p. 13107-13115

Protein and peptide engineering for chemical exchange saturation transfer imaging in the age of synthetic biology

Gilad A. A., Bar-Shir A., Bricco A. R., Mohanta Z. & McMahon M. T. (2023) NMR in Biomedicine. 36, 6, e4712.

Frontiers in 19F-MR imaging: nanofluorides and 19F-CEST as novel extensions to the 19F-MRI toolbox

Galisova A. & Bar-Shir A. (2023) Chemical Communications. 59, 37, p. 5502-5513

Novel molecular architectures for \u201cmulticolor\u201d magnetic resonance imaging

Bar-Shir A. (2023) The Israel Chemist and Chemical Engineer. 9, Tevet 5783, p. 15-23

2022

MRI reporter genes in the era of gene transfer

Cohen D., AlloucheArnon H. & BarShir A. (2022) Clinical and Translational Medicine. 12, 12, e1135.

Diffusion 19F-NMR of Nanofluorides: In Situ Quantification of Colloidal Diameters and Protein Corona Formation in Solution

Mashiach R., Avram L. & Bar-Shir A. (2022) Nano Letters. 22, 21, p. 8519-8525

Self-assembly of an MRI responsive agent under physiological conditions provides an extended time window for in vivo imaging

Tirukoti N. D., Avram L., Mashiach R., Allouche-Arnon H. & Bar-Shir A. (2022) Chemical Communications. 58, 81, p. 11410-11413

Genetically Engineered MRI-Trackable Extracellular Vesicles as SARS-CoV-2 Mimetics for Mapping ACE2 Binding in Vivo

Galisova A., Zahradnik J., Allouche-Arnon H., Morandi M. I., Abou Karam P., Fisler M., Avinoam O., Regev-Rudzki N., Schreiber G. & Bar-Shir A. (2022) ACS Nano. 16, 8, p. 12276-12289

Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression

Allouche-Arnon H., Khersonsky O., Tirukoti N. D., Peleg Y., Dym O., Albeck S., Brandis A., Mehlman T., Avram L., Harris T., Yadav N. N., Fleishman S. J. & Bar-Shir A. (2022) Nature Biotechnology. 40, 7, p. 1143-1149

2021

Cation-Ligand Complexation Mediates the Temporal Evolution of Colloidal Fluoride Nanocrystals through Transient Aggregation

Mashiach R., Weissman H., Avram-Biton L., Houben L., Diskin Posner Y., Arunachalam V., Leskes M., Rybtchinski B. & Bar-Shir A. (2021) Nano Letters. 21, 23, p. 9916-9921

Versatile non-luminescent color palette based on guest exchange dynamics in paramagnetic cavitands

Goren E., Avram L. & Bar-Shir A. (2021) Nature Communications. 12, 1, 3072.

Fast Ion-Chelate Dissociation Rate for in Vivo MRI of Labile Zinc with Frequency-Specific Encodability

Tirukoti N. D., Avram L., Haris T., Lerner B., Diskin Posner Y., Allouche-Arnon H. & Bar-Shir A. (2021) Journal of the American Chemical Society. 143, 30, p. 11751-11758

Single Fluorinated Agent for Multiplexed 19F-MRI with Micromolar Detectability Based on Dynamic Exchange

Shusterman-Krush R., Tirukoti N. D., Bandela A. K., Avram L., Allouche-Arnon H., Cai X., Gibb B. C. & Bar-Shir A. (2021) Angewandte Chemie - International Edition. 60, 28, p. 15405-15411

Glyconanofluorides as Immunotracers with a Tunable Core Composition for Sensitive Hotspot Magnetic Resonance Imaging of Inflammatory Activity

Cohen D., Mashiach R., Houben L., Galisova A., Addadi Y., Kain D., Lubart A., Blinder P., Allouche-Arnon H. & Bar-Shir A. (2021) ACS Nano. 15, 4, p. 7563-7574

Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics

Shusterman-Krush R., Grimm L., Avram L., Biedermann F. & Bar-Shir A. (2021) Chemical Science. 12, 3, p. 865-871

In situ NMR reveals real-time nanocrystal growth evolution via monomer-attachment or particle-coalescence

Mashiach R., Weissman H., Avram L., Houben L., Brontvein O., Lavie A., Arunachalam V., Leskes M., Rybtchinski B. & Bar-Shir A. (2021) Nature Communications. 12, 1, 229.

2020

Inducing defects in 19 F-nanocrystals provides paramagnetic-free relaxation enhancement for improved in-vivo hotspot MRI

Mashiach R., Cohen D., Avram L., Harris T., Pinkas I., Houben L., Allouche-Arnon H. & Bar-Shir A. (2020) Nano Letters. 20, 10, p. 7207-7212

2019

F-19-GEST NMR: studying dynamic interactions in host-guest systems

Avram L. & Bar-Shir A. (2019) Organic Chemistry Frontiers. 6, 9, p. 1503-1512

Dynamic Interactions in Synthetic Receptors: A Guest Exchange Saturation Transfer Study

Avram L., Havel V., Shusterman-Krush R., Iron M. A., Zaiss M., Sindelar V. & Bar-Shir A. (2019) Chemistry-A European Journal. 25, 7, p. 1687-1690

2018

Calcium Fluoride Nanocrystals: Tracers for In Vivo 19F Magnetic Resonance Imaging

Ashur I., Allouche-Arnon H. & Bar-Shir A. (2018) Angewandte Chemie - International Edition. 57, 25, p. 7478-7482

Quantification and tracking of genetically engineered dendritic cells for studying immunotherapy

Bar-Shir A., Alon L., Korrer M. J., Lim H. S., Yadav N. N., Kato Y., Pathak A. P., Bulte J. W. M. & Gilad A. A. (2018) Magnetic Resonance in Medicine. 79, 2, p. 1010-1019

2017

Quantifying Guest Exchange in Supramolecular Systems

Avram L., Wishard A. D., Gibb B. C. & Bar-Shir A. (2017) Angewandte Chemie - International Edition. 56, 48, p. 15314-15318

MRI-based Sensors for In Vivo Imaging of Metal Ions in Biology

Allouche-Arnon H., Tirukoti N. D. & Bar-Shir A. (2017) Israel Journal of Chemistry. 57, 9, p. 843-853

A step-wise approach for analysis of the mouse embryonic heart using 17.6 Tesla MRI

Gabbay-Benziv R., Reece E. A., Wang F., Bar-Shir A., Harman C., Turan O. M., Yang P. & Turan S. (2017) Magnetic Resonance Imaging. 35, p. 46-53

Current Landscape of diaCEST Imaging Agents

Bar-Shir A., Yang X., Song X., Pomper M. G. & McMahon M. T. (2017) Chemical Exchange Saturation Transfer Imaging : Advances and Applications . McMahon M. T.(eds.). p. 161-191

2016

Imaging the DNA alkylator melphalan by CEST MRI: An advanced approach to theranostics

Ngen E. J., Bar-Shir A., Jablonska A., Liu G., Song X., Ansari R., Bulte J. W., Janowski M., Pearl M., Walczak P. & Gilad A. A. (2016) Molecular Pharmaceutics. 13, 9, p. 3043-3053

Amplifying undetectable NMR signals to study host-guest interactions and exchange

Avram L., Iron M. & Bar-Shir A. (2016) Chemical Science. 7, 12, p. 6905-6909

2015

Fluorine-19 labeling of stromal vascular fraction cells for clinical imaging applications

Rose L. C., Kadayakkara D. K., Wang G., Bar-Shir A., Helfer B. M., OHanlon C. F., Kraitchman D. L., Rodriguez R. L. & Bulte J. W. (2015) Stem cells translational medicine. 4, 12, p. 1472-1481

Tumor-specific expression and detection of a CEST reporter gene

Minn I., Bar-Shir A., Yarlagadda K., Bulte J. W., Fisher P. B., Wang H., Gilad A. A. & Pomper M. G. (2015) Magnetic Resonance in Medicine. 74, 2, p. 544-549

Molecular Engineering of Nonmetallic Biosensors for CEST MRI

Bar-Shir A., Bulte J. W. & Gilad A. A. (2015) ACS Chemical Biology. 10, 5, p. 1160-1170

Advances in using MRI probes and sensors for in vivo cell tracking as applied to regenerative medicine

Srivastava A. K., Kadayakkara D. K., Bar-Shir A., Gilad A. A., McMahon M. T. & Bulte J. W. M. (2015) Disease Models & Mechanisms. 8, 4, p. 323-336

Label-free in vivo molecular imaging of underglycosylated mucin-1 expression in tumour cells

Song X., Airan R. D., Arifin D. R., Bar-Shir A., Kadayakkara D. K., Liu G., Gilad A. A., van Zijl Z. P. C. M., McMahon M. T. & Bulte J. W. M. (2015) Nature Communications. 6, 6719.

Supercharged green fluorescent proteins as bimodal reporter genes for CEST MRI and optical imaging

Bar-Shir A., Liang Y., Chan K. W., Gilad A. A. & Bulte J. W. (2015) Chemical Communications. 51, 23, p. 4869-4871

Label-free imaging of gelatin-containing hydrogel scaffolds

Liang Y., Bar-Shir A., Song X., Gilad A. A., Walczak P. & Bulte J. W. M. (2015) Biomaterials. 42, p. 144-150

Biophysical characterization of human protamine-1 as a responsive CEST MR contrast agent

Oskolkov N., Bar-Shir A., Chan K. W. Y., Song X., van Zijl P. C. M., Bulte J. W. M., Gilad A. A. & McMahon M. T. (2015) ACS Macro Letters. 4, 1, p. 34-38

Single 19F probe for simultaneous detection of multiple metal ions using miCEST MRI

Bar-Shir A., Yadav N. N., Gilad A. A., van Zijl P. C. M., McMahon M. T. & Bulte J. W. M. (2015) Journal of the American Chemical Society. 137, 1, p. 78-81

2014

Natural D-glucose as a biodegradable MRI relaxation agent

Yadav N. N., Xu J., Bar-Shir A., Qin Q., Chan K. W. Y., Grgac K., Li W., McMahon M. T. & van Zijl P. C. M. (2014) Magnetic Resonance in Medicine. 72, 3, p. 823-828

Alginate-coated magnetic nanoparticles for noninvasive MRI of extracellular calcium

Bar-Shir A., Avram L., Yariv-Shoushan S., Anaby D., Cohen S., Segev-Amzaleg N., Frenkel D., Sadan O., Offen D. & Cohen Y. (2014) NMR in Biomedicine. 27, 7, p. 774-783

Variable delay multi-pulse train for fast chemical exchange saturation transfer and relayed-nuclear overhauser enhancement MRI

Xu J., Yadav N. N., Bar-Shir A., Jones C. K., Chan K. W. Y., Zhang J., Walczak P., McMahon M. T. & van Zijl P. C. M. (2014) Magnetic Resonance in Medicine. 71, 5, p. 1798-1812

Human protamine-1 as an mri reporter gene based on chemical exchange

Bar-Shir A., Liu G., Chan K. W. Y., Oskolkov N., Song X., Yadav N. N., Walczak P., McMahon M. T., van Zijl P. C. M., Bulte J. W. M. & Gilad A. A. (2014) ACS Chemical Biology. 9, 1, p. 134-138

2013

Metal ion sensing using ion chemical exchange saturation transfer 19F magnetic resonance imaging

Bar-Shir A., Gilad A. A., Chan K. W. Y., Liu G., van Zijl P. C. M., Bulte J. W. M. & McMahon M. T. (2013) Journal of the American Chemical Society. 135, 33, p. 12164-12167

Transforming thymidine into a magnetic resonance imaging probe for monitoring gene expression

Bar-Shir A., Liu G., Liang Y., Yadav N. N., McMahon M. T., Walczak P., Nimmagadda S., Pomper M. G., Tallman K. A., Greenberg M. M., van Zijl P. C. M., Bulte J. W. M. & Gilad A. A. (2013) Journal of the American Chemical Society. 135, 4, p. 1617-1624

Synthesis of a probe for monitoring HSV1-tk reporter gene expression using chemical exchange saturation transfer MRI

Bar-Shir A., Liu G., Greenberg M. M., Bulte J. W. M. & Gilad A. A. (2013) NATURE PROTOCOLS. 8, 12, p. 2380-2391

2012

MRI biosensor for protein kinase A encoded by a single synthetic gene

Airan R. D., Bar-Shir A., Liu G., Pelled G., McMahon M. T., van Zijl P. C. M., Bulte J. W. M. & Gilad A. A. (2012) Magnetic Resonance in Medicine. 68, 6, p. 1919-1923

Early in vivo MR spectroscopy findings in organophosphate-induced brain damage-potential biomarkers for short-term survival

Shrot S., Anaby D., Krivoy A., Makarovsky I., Rosman Y., Bloch-Shilderman E., Lazar S., Bar-Shir A. & Cohen Y. (2012) Magnetic Resonance in Medicine. 68, 5, p. 1390-1398

Use of MR cell tracking to evaluate targeting of glial precursor cells to inflammatory tissue by exploiting the very late antigen-4 docking receptor

Gorelik M., Orukari I., Wang J., Gilad A. A., Galpoththawela S., Bar-Shir A., Kim H., Walczak P., Levy M., Bulte J. W. M., Kerr D. A. & Levchenko A. (2012) Radiology. 265, 1, p. 175-185

Detection of rapidly exchanging compounds using on-resonance frequency-labeled exchange (FLEX) transfer

Yadav N. N., Jones C. K., Xu J., Bar-Shir A., Gilad A. A., McMahon M. T. & van Zijl P. C. M. (2012) Magnetic Resonance in Medicine. 68, 4, p. 1048-1055

CEST phase mapping using a length and offset varied saturation (LOVARS) scheme

Song X., Gilad A. A., Joel S., Liu G., Bar-Shir A., Liang Y., Gorelik M., Pekar J. J., van Zijl P. C. M., Bulte J. W. M. & McMahon M. T. (2012) Magnetic Resonance in Medicine. 68, 4, p. 1074-1086

2011

Multimodal imaging of sustained drug release from 3-D poly(propylene fumarate) (PPF) scaffolds

Choi J., Kim K., Kim T., Liu G., Bar-Shir A., Hyeon T., McMahon M. T., Bulte J. W. M., Fisher J. P. & Gilad A. A. (2011) Journal of Controlled Release. 156, 2, p. 239-245

Monitoring enzyme activity using a diamagnetic chemical exchange saturation transfer magnetic resonance imaging contrast agent

Liu G., Liang Y., Bar-Shir A., Chan K. W. Y., Galpoththawela C. S., Bernard S. M., Tse T., Yadav N. N., Walczak P., McMahon M. T., Bulte J. W. M., van Zijl P. C. M. & Gilad A. A. (2011) Journal of the American Chemical Society. 133, 41, p. 16326-16329

Optogenetic-guided cortical plasticity after nerve injury

Li N., Downey J. E., Bar-Shir A., Gilad A. A., Walczak P., Kim H., Joel S. E., Pekar J. J., Thakor N. V. & Pelled G. (2011) Proceedings of the National Academy of Sciences of the United States of America. 108, 21, p. 8838-8843

2010

Late stimulation of the sphenopalatine-ganglion in ischemic rats: Improvement in N-acetyl-aspartate levels and diffusion weighted imaging characteristics as seen by MR

Bar-Shir A., Shemesh N., Nossin-Manor R. & Cohen Y. (2010) Journal of Magnetic Resonance Imaging. 31, 6, p. 1355-1363

2009

QSI and DTI of excised brains of the myelin-deficient rat

Bar-Shir A., Duncan I. D. & Cohen Y. (2009) NeuroImage. 48, 1, p. 109-116

Observation of restricted diffusion in the presence of a free diffusion compartment: Single- and double-PFG experiments

Shemesh N., Oezarslan E., Bar-Shir A., Basser P. J. & Cohen Y. (2009) Journal of Magnetic Resonance. 200, 2, p. 214-225

2008

Three-dimensional water diffusion in impermeable cylindrical tubes: Theory versus experiments

Avram L., Özarslan E., Assaf Y., Bar-Shir A., Cohen Y. & Basser P. J. (2008) NMR in Biomedicine. 21, 8, p. 888-898

Crossing fibers, diffractions and nonhomogeneous magnetic field: correction of artifacts by bipolar gradient pulses

Bar-Shir A. & Cohen Y. (2008) Magnetic Resonance Imaging. 26, 6, p. 801-808

Reversal of axonal loss and disability in a mouse model of progressive multiple sclerosis

Basso A. S., Frenkel D., Quintana F. J., Costa-Pinto F. A., Petrovic-Stojkovic S., Puckett L., Monsonego A., Bar-Shir A., Engel Y., Gozin M. & Weiner H. L. (2008) Journal of Clinical Investigation. 118, 4, p. 1532-1543

High b-value g-space diffusion MRS of nerves: Structural information and comparison with histological evidence

Bar-Shir A. & Cohen Y. (2008) NMR in Biomedicine. 21, 2, p. 165-174

2005

Synthesis and water solubility of adamantyl-OEG-fullerene hybrids

Bar-Shir A., Engel Y. & Gozin M. (2005) Journal of Organic Chemistry. 70, 7, p. 2660-2666