(#equal contribution, *corresponding)


Abundo, MP, Tifrea AT, Buss MT, Barturen-Larrea P, Jin Z, Malounda D, Shapiro MG*. Ultrasound-actuated drug delivery with acoustic percolation switches. bioRxiv preprint

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


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


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


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).

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


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


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


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


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


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).

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).


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

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