(#equal contribution, *corresponding)
2024
Jin Z, Lakshmanan A#, Zhang R#, Tran TA, Rabut C, Dutka P, Duan M, Hurt RC, Malounda D, Yao Y, Shapiro MG*. Ultrasonic reporters of calcium for deep tissue imaging of cellular signals. bioRxiv preprint
Hurt RC#, Jin Z#, Soufi M, Wong KK, Sawyer DP, Shen HK, Dutka P, Deshpande R, Zhang R, Mittelstein DR, Shapiro MG*. Directed evolution of acoustic reporter genes using high-throughput acoustic screening. . bioRxiv preprint
Schrunk E, Dutka P, Hurt RC, Malounda D, Wi D*, Shapiro MG*. Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures. Bioconjugate Chemistry 35, 333 (2024). article
Ling B, Gungoren B, Yao Y, Dutka P, Smith CAB, Lee J, Swift MB, Shapiro MG*. Truly tiny acoustic biomolecules for ultrasound imaging and therapy. Advanced Materials (2024). article
2023
Rabut C#, Norman S#*, Griggs W#, Russin JJ, Jan K, Christopoulos V, Liu C*, Andersen RA*, Shapiro MG*. A window to the brain: ultrasound imaging of human neural activity through a permanent acoustic window. bioRxiv preprint
Duan M#, Dev I#, Lu A, Yi MY, Shapiro MG*. Stoichiometric expression of messenger polycistrons by eukaryotic ribosomes (SEMPER) for compact, ratio-tunable multi-gene expression from single mRNAs. bioRxiv preprint
Griggs WS#, Norman SL#, Deffieux T, Segura F, Osmanski BF, Chau G, Christopoulos V, Liu C, Tanter M, Shapiro MG, Andersen RA. Decoding motor plans using a closed-loop ultrasonic brain-machine interface. Nature Neuroscience (2023) article | press
Ling B#, Ko JH#, Stordy B, Zhang Y, Didden TF, Malounda D, Swift MB, Chan WCW, Shapiro MG*. Gas vesicle-blood interactions enhance ultrasound imaging contrast. Nano Letters 23, 10748 (2023). article
Guo H, Salahshoor H, Wu D, Yoo S, Sato T, Tsao D, Shapiro MG*. Effects of focused ultrasound in a “clean” mouse model of ultrasonic neuromodulation. iScience 26, 108372 (2023). article
Kim WS#, Min S#, Kim SK, Kang S, An S, Criado-Hidalgo E, Davis HC, Bar-Zion A, Malounda D, Kim YH, Lee JH, Bae SH, Lee JG, Kwak M, Cho SW*, Shapiro MG*, Cheon J*. Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo. Nature Materials (2023). article
Yao Y, McFadden ME, Luo, SM, Barber RW, Kang E, Bar-Zion A, Smith CAB, Jin Z, Legendre M, Ling B, Malounda D, Torres A, Hamza T, Edwards CER, Shapiro MG*, Robb MJ*. Remote control of mechanochemical reactions under physiological conditions using biocompatible focused ultrasound. PNAS 120, e2309822120 (2023). article | press
Dutka P, Metskas LA, Hurt RA, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TS, Shapiro MG*, Jensen GJ*. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 31, 518 (2023) article
Wu D, Baresch D, Cook C, Duan M, Malounda D, Maresca D, Abundo MP, Lee J, Shivaei S, Mittelstein DR, Qiu T, Fischer P, Shapiro MG*. Biomolecular actuators for genetically selective acoustic manipulation of cells. Science Advances 9, eadd9186 (2023). article | press | video
Hurt RC#, Buss MT#, Duan M#, Wong K, You MY, Sawyer DP, Swift MB, Dutka P, Barturen-Larrea P, Mittelstein DR, Jin Z, Abedi MH, Farhadi A, Dephande R, Shapiro MG*. Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria. Nature Biotechnology 41, 919 (2023). article | research briefing
Sharma S, Ramadi KB, Poole N, Srinivasan S, Ishida K, Kuosmanen J, Jenkins J, Aghlmand F, Swift MB, Shapiro MG, Traverso G, Emami A*. Location-aware ingestible microdevices for wireless monitoring of gastrointestinal dynamics. Nature Electronics 6, 242 (2023). article
Liang W, Guo H, Mittelstein DR, Shapiro MG, Shimojo S, Shehata MH*. Auditory Mondrian masks the airborne-auditory artifact of focused ultrasound stimulation in humans. Brain Stimulation 16, 604 (2023). article
Xiong LL, Garrett MA, Kornfield JA*, Shapiro MG*. Living material with temperature-dependent light absorption. Advanced Science 2301730 (2023) article
Sharma S, Melton H, Edmonds L, Addington O, Shapiro MG, Emami A*. A monolithic 3D magnetic sensor in 65nm CMOS with <10μTrms noise and 14.8μW power. IEEE CICC (2023). article
2022
Salahshoor H#, Yao Y#, Dutka P#, Nyström NN, Jin Z, Min E, Malounda D, Jensen G, Ortiz M, Shapiro MG*. Geometric effects in gas vesicle buckling under ultrasound. Biophysical Journal 121, 4221 (2022). article
Xiong LL, Garrett MA, Buss MT, Kornfield JA, Shapiro MG*. Tunable temperature-sensitive transcriptional activation based on Lambda repressor. ACS Synthetic Biology 11, 2518 (2022). article
Abedi MH#, Yao M#, Mittelstein DR, Bar-Zion A, Swift MB, Lee-Gosselin A, Barturen-Larrea P, Buss MT, Shapiro MG*. Ultrasound-controllable engineered bacteria for cancer immunotherapy. Nature Communications 13, 1585 (2022). article
Yoo S, Mittelstein DR, Hurt RC, Lacroix JJ, Shapiro MG*. Focused ultrasound excites cortical neurons via mechanosensitive calcium accumulation and ion channel amplification. Nature Communications 13, 493 (2022). article | readcube
Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geshwind DH, Holschneider DP, Fiscbach MA, Mazmanian SK*. A gut-derived metabolite alters brain activity and anxiety behaviour in mice. Nature 602, 647 (2022). article
Salahshoor H, Guo H, Shapiro MG, Ortiz M*. Mechanics of ultrasonic neuromodulation in a mouse subject. Extreme Mechanics Letters 50, 101539 (2022). article
Anthis AHC, Abundo MP, Neuer AL, Tsolaki E, Rosendorf J, Rduch T, Starsich FHL, Liska V, Schlegel AA, Shapiro MG, Herrmann IK*. Modular stimuli-responsive hydrogel sealants for early gastrointestinal leak detection and containment. Nature Communications 13, 7311 (2022). article
2021
Bar-Zion A*, Solomon O, Rabut C, Maresca D, Eldar YC, Shapiro MG. Doppler slicing for ultrasound super-resolution without contrast agents. bioRxiv preprint
Bar-Zion A, Nourmahnad A, Mittelstein DR, Shivaei S, Yoo S, Buss MT, Hurt RC, Malounda D, Abedi MH, Lee-Gosselin A, Swift MB, Maresca D, Shapiro MG*. Acoustically triggered mechanotherapy using genetically encoded gas vesicles. Nature Nanotechnology 16, 1403–1412 (2021). article | readcube
Sawyer DP, Bar-Zion A, Farhadi A, Shivaei S, Ling B, Lee-Gosselin A, Shapiro MG*. Ultrasensitive ultrasound imaging of gene expression with signal unmixing. Nature Methods 18, 945-952 (2021). article | readcube | press
Li H, Heath JE, Trippett JS, Shapiro MG*, Szablowski JO*. Engineering viral vectors for acoustically targeted gene delivery. bioRxiv preprint
Rabut C, Wu D, Ling B, Jin Z, Malounda D, Shapiro MG*. Ultrafast amplitude modulation for molecular and hemodynamic ultrasound imaging. Applied Physics Letters 118, 244102 (2021). article | bioRxiv preprint
Yao Y, Jin Z, Ling B, Malounda D, Shapiro MG*. Self-assembly of protein superstructures by physical interactions under cytoplasm-like conditions. Biophysical Journal 120, 2701-2709 (2021). article
Norman SL#, Maresca D#, Christopoulos VN#, Griggs WS, Demene C, Tanter M, Shapiro MG*, Andersen RA*. Single-trial decoding of movement intentions using functional ultrasound neuroimaging. Neuron 109, 1554-1566 (2021).
article | press | bioRxiv preprint
Buss MT#, Ramesh P#, English MA, Lee-Gosselin A, Shapiro MG*. Spatial control of probiotic bacteria in the gastrointestinal tract assisted by magnetic particles. Advanced Materials 33, 2007473 (2021).
article
Farhadi A, Sigmund F, Westmeyer GG*, Shapiro MG*. Genetically encodable materials for non-invasive biological imaging. Nature Materials 20, 585-592 (2021). article | readcube
Sharma S*, Telikicherla A; Ding G; Aghlmand F; Hashemi Talkhooncheh A; Shapiro MG, Emami A. Wireless 3D surgical navigation and tracking system with 100 µm accuracy using magnetic-field gradient-based localization. IEEE Transactions on Medical Imaging (2021). article
Dutka P, Malounda D, Metskas LA, Chen S, Hurt RC, Lu GJ, Jensen GJ*, Shapiro MG*. Measuring gas vesicle dimensions by electron microscopy. Protein Science 30, 1081-86 (2021). article | bioRxiv preprint
2020
Rabut C, Yoo S, Hurt RC, Jin Z, Guo H, Ling B, Shapiro MG*. Ultrasound technologies for imaging and modulating neural activity. Neuron 108, 93-110 (2020). article
Ling B, Lee J, Maresca D, Lee-Gosselin A, Malounda D, Swift MB, Shapiro MG*. Biomolecular ultrasound imaging of phagolysosomal function. ACS Nano 14, 12210-12221 (2020). article
Abedi MH, Lee J, Piraner DI, Shapiro MG*. Thermal control of engineered T-cells. ACS Synthetic Biology 9, 1941-50 (2020). article | bioRxiv preprint
Lakshmanan A#, Jin Z#, Nety SP, Sawyer DP, Lee-Gosselin A, Malounda D, Swift MB, Maresca D, Shapiro MG*. Acoustic biosensors for ultrasound imaging of enzyme activity. Nature Chemical Biology 16, 988-96 (2020).
article | readcube | behind the paper | press
Salahshoor H*, Shapiro MG*, Ortiz M*. Transcranial focused ultrasound generates skull-conducted shear waves: computational model and implications for neuromodulation. Applied Physics Letters 117, 033702 (2020). article | bioRxiv preprint
Davis HC, Kang SW, Lee JH, Shin TH, Putterman H, Cheon J, Shapiro MG*. Nanoscale heat transfer from magnetic nanoparticles and ferritin in an alternating magnetic field. Biophysical Journal 118, 1502-1510 (2020). article
Farhadi A#, Bedrossian M#, Lee J, Ho GH, Shapiro MG*, Nadeau J*. Genetically encoded phase contrast agents for digital holographic microscopy. Nano Letters (2020). article
Figueroa-Schibber E, Mittelstein DF, Gharib M, Shapiro MG, Lee PP, Ortiz M*. A dynamical model of oncotripsy by mechanical cell fatigue: selective cancer cell ablation by low-intensity pulsed ultrasound. Proceedings of the Royal Society A 476, 20190692 (2020). article
Zhang S#, Huang A#, Bar‐Zion A, Wang J, Vazquez Mena O, Shapiro MG, Friend J*. The vibration behavior of sub‐micrometer gas vesicles in response to acoustic excitation determined via laser doppler vibrometry. Advanced Functional Materials 2020, 2000239 (2020). article
Lu GJ, Chou L, Malounda D, Patel AK, Welsbie DS, Chou DL*, Ramalingam T*, Shapiro MG*. Genetically encodable contrast agents for optical coherence tomography. ACS Nano 14, 7, 7823-7831 (2020). article | bioRxiv preprint
Mittelstein DR, Ye J, Figueroa-Schibber E, Roychoudhury A, Troyas-Martinez L, Fekrazad MH, Ortiz M, Lee PP, Shapiro MG*, Grarib M*. Selective ablation of cancer cells with low intensity pulsed ultrasound. Applied Physics Letters 116, 013701 (2020). article
2019
Bar-Zion A, Nourmahnad A, Mittelstein DR, Yoo S, Malounda D, Abedi MH, Lee-Gosselin A, Maresca D, Shapiro MG*. Acoustically detonated biomolecules for genetically encodable inertial cavitation. bioRxiv preprint
Maresca D, Payen T, Lee-Gosselin A, Ling B, Malounda D, Demene C, Tanter M, Shapiro MG*. Acoustic biomolecules enhance hemodynamic functional ultrasound imaging of neural activity. NeuroImage 209, 116467 (2019). article
Farhadi A, Ho GH, Sawyer DP, Bourdeau RW, Shapiro MG*. Ultrasound imaging of gene expression in mammalian cells. Science 365, 1469-1475 (2019). article | perspective | press
Piraner DI, Wu Y, Shapiro MG*. Modular thermal control of protein dimerization. ACS Synthetic Biology 8, 2256-2262 (2019). article
Szablowski JO#, Bar-Zion A#, Shapiro MG*. Achieving spatial and molecular specificity with ultrasound-targeted biomolecular nanotherapeutics. Accounts of Chemical Research 52, 2427 – 2434 (2019). article
2018
Maresca D#*, Sawyer DP#, Renaud G, Lee-Gosselin A, Shapiro MG*. Nonlinear X-wave ultrasound imaging of acoustic biomolecules. Physical Review X 8, 041002 (2018).
article | synopsis
Ramesh P, Hwang SJ, Davis HC, Lee-Gosselin A, Bharadwaj V, English MA, Sheng J, Iyer V, Shapiro MG*. Ultraparamagnetic cells formed through intracellular oxidation and chelation of paramagnetic iron. Angewandte Chemie 57, 12385-12389 (2018). article
Kunth M, Lu GJ, Witte C, Shapiro MG*, Schröder L*. Protein nanostructures produce self-adjusting hyperpolarized magnetic resonance imaging contrast through physical gas partitioning. ACS Nano 12, 10939-10948 (2018). article
Szablowski JO, Lue B, Lee-Gosselin A, Malounda D, Shapiro MG*. Acoustically targeted chemogenetics for the non-invasive control of neural circuits.
Nature Biomedical Engineering 2, 475-484 (2018).
article | readcube | news and views | press | behind the paper
Sato T*, Shapiro MG#*, Tsao DY#*. Ultrasonic neuromodulation causes widespread cortical activation via an indirect auditory mechanism. Neuron 98, 1031-1041 (2018). article | companion article
Lu GJ, Farhadi A, Szablowski JO, Lee-Gosselin A, Barnes SR, Lakshmanan A, Bourdeau RW, Shapiro MG*. Acoustically modulated magnetic resonance imaging of gas-filled protein nanostructures. Nature Materials 17, 456–463 (2018).
article | readcube | news and views | press | behind the paper
Maresca D#, Lakshmanan A#, Abedi M, Bar-Zion A, Farhadi A, Lu GJ, Szablowski JO, Wu D, Yoo S, Shapiro MG*. Biomolecular ultrasound and sonogenetics. Annual Review of Chemical and Biomolecular Engineering 9, 229-252 (2018). article
Lu GJ#, Farhadi A#, Mukherjee A, Shapiro MG*. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging. Current Opinion in Chemical Biology 45, 57-63 (2018). article
Farhadi A, Ho G, Kunth M, Ling B, Lakshmanan A, Lu GJ, Bourdeau RW, Schröder L, Shapiro MG*. Recombinantly expressed gas vesicles as nanoscale contrast agents for ultrasound and hyperpolarized MRI. AIChE Journal 64, 2927-2933 (2018). article
Davis HC#, Ramesh P#, Bhatnagar A, Lee-Gosselin A, Barry JF, Glenn DR, Walsworth RL, Shapiro MG*. Mapping the microscale origins of MRI contrast with subcellular NV diamond magnetometry. Nature Communications 9, 131 (2018). article | press
Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Ravindra Kumar S, Nety SP, Shapiro MG*. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts. Nature 553, 86–90 (2018).
article | readcube | news and views | press | behind the paper
Le Floc’h J*, Zlitni A, Bilton HA, Yin M, Farhadi A, Janzen NR, Shapiro MG, Valliant JF*, Foster FS. In vivo biodistribution of radiolabeled acoustic protein nanostructures. Molecular Imaging and Biology 20, 230-239 (2018). article
2017
Monge M, Lee-Gosselin A, Shapiro MG*, Emami A*. Localization of microscale devices in vivo using addressable transmitters operated as magnetic spins. Nature Biomedical Engineering 1, 736-744 (2017).
article | readcube | news and views | press | behind the paper
Lakshmanan A#, Lu GJ#, Farhadi A#, Nety SP#, Kunth M, Lee-Gosselin A, Maresca D, Bourdeau RW, Yin M, Yan J, Witte C, Malounda D, Foster FS, Schröder L, Shapiro MG*. Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI. Nature Protocols 12, 2050-2080 (2017). article | readcube
Piraner DI, Farhadi A, Davis HC, Wu D, Maresca D, Szablowski JO, Shapiro MG*. Going deeper: biomolecular tools for acoustic and magnetic imaging and control of cellular function. Biochemistry (2017). article
Ojala DS, Sun S, Santiago-Ortiz JL, Shapiro MG, Romero PA, Schaffer DV*. In vivo selection of a computationally designed SCHEMA AAV library yields a novel variant for infection of adult neural stem cells in the SVZ. Molecular Therapy 26, 304-319 (2017). article
Maley AM, Lu GJ, Shapiro MG, Corn RM*. Characterizing single polymeric and protein nanoparticles with surface plasmon resonance imaging measurements. ACS Nano 11, 7447-7456 (2017). article
Mukherjee A, Davis HC, Ramesh P, Lu GJ, Shapiro MG*. Biomolecular MRI reporters: evolution of new mechanisms. Progress in NMR Spectroscopy 102-103, 32-42 (2017). article
Cherin E*, Melis JM, Bourdeau RW, Yin M, Kochmann DM, Foster FS#, Shapiro MG#. Acoustic behavior of Halobacterium salinarum gas vesicles in the high frequency range: experiments and modeling. Ultrasound in Medicine and Biology 43, 1016-1030 (2017). article
Maresca D, Lakshmanan A, Lee-Gosselin A, Melis JM, Ni YL, Bourdeau RW, Kochmann DM, Shapiro MG*. Nonlinear ultrasound imaging of nanoscale acoustic biomolecules. Applied Physics Letters 110, 073704 (2017). article
Gilad AA*, Shapiro MG*. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging. Molecular Imaging and Biology 19, 373-378 (2017). article
Piraner DI#, Abedi MH#, Moser BA, Lee-Gosselin A, Shapiro MG*. Tunable thermal bioswitches for in vivo control of microbial therapeutics. Nature Chemical Biology 13, 75-80 (2017). article | press | video | highlight in Nature Methods
2016
Mukherjee A#, Wu D#, Davis HC, Shapiro MG*. Noninvasive imaging using reporter genes altering cellular water permeability. Nature Communications 7, 13891 (2016). article | press | highlight in Lab Animal
Barksiy DA, Goodson BM, Branca RT, Lu GJ, Shapiro MG, Schröder L, Chekmenev EY*, et al. NMR hyperpolarization techniques of gases. Chemistry–A European Journal 23, 725-751 (2016).
article
Lakshmanan A, Farhadi A, Nety SP, Lee-Gosselin A, Bourdeau RW, Maresca D, Shapiro MG*. Molecular engineering of acoustic protein nanostructures. ACS Nano 10, 7314-22 (2016).
article | press
2014
Shapiro MG*, Ramirez RM, Sperling LJ, Sun G, Pines A, Schaffer DV, Bajaj VS*. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. Nature Chemistry 6, 629-34 (2014). article | commentary in Science Translational Medicine
Shapiro MG*, Goodwill PW, Neogy A, Yin M, Foster FS, Schaffer DV, Conolly SM. Biogenic gas nanostructures as ultrasonic molecular reporters. Nature Nanotechnology 9, 311-6 (2014). article | news and views
2013 and earlier
Marblestone AH, Zamft BM, Shapiro MG, Boyden ES, Church GM, Kording KP, et al. Physical Principles for Scalable Neural Recording. Frontiers in Computational Neuroscience (2013). article
Shapiro MG*, Priest MF, Siegel PH, Bezanilla F*. Thermal mechanisms of millimeter wave stimulation of excitable cells. Biophysical Journal (2013). article
Romero PA, Shapiro MG, Arnold FH, Jasanoff A. Directed evolution of protein-based neurotransmitter sensors for MRI. Methods in Molecular Biology 995, 193-205 (2013). article
Shapiro MG*, Frazier SJ, Lester HA. Unparalleled control of neural activity using orthogonal pharmacogenetics. ACS Chemical Neuroscience (2012). article
Shapiro MG, Homma K, Villarreal S, Richter CP, Bezanilla F. Infrared light excites cells by changing their electrical capacitance. Nature Communications 3:736 (2012). article
Shapiro MG, Westmeyer GG, Romero PA, Szablowski JO, Küster B, Shah A, Otey CR, Langer R, Arnold FH, Jasanoff A. Directed evolution of a magnetic resonance imaging contrast agent for noninvasive imaging of dopamine. Nature Biotechnology 28, 264-70 (2010). article
Shapiro MG, Szablowsky JO, Langer R, Jasanoff A. Protein nanoparticles engineered to sense kinase activity in MRI. Journal of the American Chemical Society 131, 2484-6 (2009). article
Shapiro MG, Atanasijevich T, Faas H, Westmeyer GG, Jasanoff A. Dynamic imaging with MRI contrast agents: quantitative considerations. Magnetic Resonance Imaging 24, 449-62 (2006). article
