{"id":23,"date":"2018-01-09T00:16:44","date_gmt":"2018-01-09T08:16:44","guid":{"rendered":"https:\/\/shapirolabnew.che.caltech.edu\/?page_id=23"},"modified":"2026-02-06T15:22:15","modified_gmt":"2026-02-06T23:22:15","slug":"publications","status":"publish","type":"page","link":"https:\/\/shapirolab.caltech.edu\/?page_id=23","title":{"rendered":"Publications"},"content":{"rendered":"

(#equal contribution, *corresponding)<\/p>\n

2025<\/span><\/span><\/strong><\/p>\n

Nystr\u00f6m NN, Jin Z, Bennett ME, Zhang R, Swift MB, Shapiro MG*. Multiplexed ultrasound imaging of gene expression<\/strong>. Nature Methods<\/em> (2025). article<\/a><\/p>\n

Schrunk E, Lee S, Dutka P, Wu D*, Shapiro MG*. Sono-uncaging for spatiotemporal control of chemical reactivity<\/strong>. JACS<\/em> 147, 35422 (2025). article<\/a><\/p>\n

Liu A, Farooq AS, Abedi MH, Smith CAB, Wu D*, Shapiro MG*. Thermally controlled state switches for macrophage immunotherapy<\/strong>. ACS Synthetic Biology<\/em> 14, 4304 (2025). article<\/a><\/p>\n

Buss MT, Zhu L, Kwon JH, Tabor JJ, Shapiro MG*. Probiotic acoustic biosensors for noninvasive imaging of gut inflammation<\/strong>. Nature Communications<\/em> 16, 7931 (2025). article<\/a><\/p>\n

\"\"<\/a>Heiles B, Nelissen F, Terwiel D, Park BM, Munoz Ibarra E, Matalliotakis A, Waasdorp R, Ara T, Barturen-Larrea P, Duan M, Shapiro MG, Gazzola V, Maresca D*. Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale<\/strong>. Science<\/em> 388, eads1325 (2025). article<\/a><\/p>\n

Abundo, MP, Tifrea AT, Buss MT, Barturen-Larrea P, Jin Z, Malounda D, Shapiro MG*. Acoustic percolation switches enable targeted drug delivery controlled by diagnostic ultrasound<\/strong>. PNAS<\/em> 122 (20) e2423078122 (2025). article<\/a><\/p>\n

Davoodi E, Li J, Ma X, Hasani Najafabadi A, Yoo J, Lu G, Shirzaei Sani E, Lee S, Montazerian H, Kim G, Williams J, Yang JW, Zeng Y, Li LS, Jin Z, Sadri B, Nia SS, Wang LV, Hsiai TK, Weiss PS, Zhou Q, Khademhosseini A, Wu D, Shapiro MG, Gao W*. Imaging-guided deep tissue in vivo sound printing<\/strong>. Science<\/em> 388, 616 (2025). article<\/a><\/p>\n

\"\"<\/a>Cheung KYM, Nair A, Li L, Shapiro MG, Anderson DJ*. Population coding of predator imminence in the hypothalamus<\/strong>. Neuron<\/em> 113, 1259 (2025). article<\/a>
\n 
\n <\/p>\n

Smith CAB, Toulemonde M, Lerendegui M, Riemer K, Malounda D, Weinberg P, Shapiro MG*, Tang MX*. Enhanced ultrasound image formation with computationally efficient cross-angular delay multiply and sum beamforming<\/strong>. Ultrasound in Medicine and Biology<\/em> 51, 1523(2025). article<\/a><\/p>\n

Zhang G, Vert M, Nouhoum M, Rivera E, Haidour N, Jimenez A, Deffieux T, Barral S, Hersen P, Pezet S, Rabut C, Shapiro MG, Tanter M*. Amplitude-Modulated Singular Value Decomposition for Ultrafast Ultrasound Imaging of Gas Vesicles<\/strong>. IEEE TMI<\/em> TMI.2025.3565023 (2025). article<\/a><\/p>\n

Smith CAB, Duan MT, Yan J, Taylor L, Shapiro MG, Tang MX*. Achieving single cell acoustic localisation with deactivation super resolution<\/strong>. npj Acoustics<\/em> 1, 5 (2025). article<\/a><\/p>\n

Ge X, Wekselblatt JB, Elmore S, Wang B, Wang T, Dai T, Zhang T, Dave H, Ghaderi M, Anilkumar AR, Wang B, Sirsi SR, Ahn JM, Shapiro MG, Oka Y, Lois C, Qin ZP*. In Vivo Cytosolic Delivery of Biomolecules into Neurons for Super\u2010Resolution Imaging and Genome Modification<\/strong>. Advanced Science<\/em> 2501033 (2025). article<\/a><\/p>\n

Smith CAB, Bar-Zion A, Wu Q, Malounda D, Bau L, Stride E*, Shapiro MG*, Coussios CC*. Ultrafast optical and passive acoustic mapping characterization of nanoscale cavitation nuclei based on gas vesicle proteins<\/strong>. AIP Advances<\/em> 15, 025016 (2025). article<\/a><\/p>\n

Stordy BP, Sepahi Z, Patr\u00f3n GD, Yang W, Goodson AD, Blackadar C, Tavares AJ, Lin G, Malekjahani A, Ling B, Ravichandran R, Hicks DR, Shapiro MG, Zhang M, King NP, Baker D, Ricardez-Sandoval LA, Chan WCW*. The Binding Affinities of Serum Proteins to Nanoparticles<\/strong>. JACS<\/em> jacs.5c02576 (2025). article<\/a><\/p>\n

Yang JW, Jin Z, Wang TY, Shapiro MG*. Ultrasonic reporter of kinase activity<\/strong>. bioRxiv preprint<\/a><\/p>\n

Li H, Pavlic A, Ibrahim NE, Wu D*, Shapiro MG*. Rewiring protein function through genetically encoded oxidative chemistry<\/strong>. bioRxiv preprint<\/a><\/p>\n

Rabut C*, Shivaei S, Heiles B, Shapiro MG*. Trimodal brain-wide ultrasound imaging of brain-tumor interaction<\/strong>. bioRxiv preprint<\/a><\/p>\n

Shivaei S, Cheung KYM, Yadav A, Hurvitz IU, Lee S, Revilla J, Rabut C, Criado-Hidalgo, Zhang RJ, Shapiro MG*. Ultrasound imaging of in situ transcriptional activity in opaque tissue<\/strong>. bioRxiv preprint<\/a><\/p>\n

Rabut C, Daghlian GH, Barturen-Larrea P, Li HR, Vorder Bruegge R, Jones RM, Malounda D, Pinton GF, Shapiro MG*. Acoustic tumor paint for real-time imaging, surgical guidance and recurrence monitoring of brain tumors with ultrasound<\/strong>. bioRxiv preprint<\/a><\/p>\n

Lee S, Wu D, Malounda D, Rabut C*, Shapiro MG*. Real-time volumetric imaging of cells and molecules in deep tissues with Takoyaki ultrasound<\/strong>. bioRxiv preprint<\/a><\/p>\n

Shivaei S, Liu A, Abedi MH, Revilla J, Hurvitz IU, Swift MB, Shapiro MG*. Non-invasive imaging of cell-based therapies using acoustic reporter genes<\/strong>. bioRxiv preprint<\/a><\/p>\n

Tolooshams B, Lin L, Callier T, Wang J, Pal S, Chandrashekar A, Rabut C, Li Z, Blagden C, Norman SL, Azizzadenesheli K, Liu C, Shapiro MG, Andersen RA*, Anandkumar A*. VARS-fUSI: Variable Sampling for Fast and Efficient Functional Ultrasound Imaging using Neural Operators<\/strong>. bioRxiv preprint<\/a><\/p>\n

2024<\/span><\/span><\/strong><\/p>\n

Strohm EM, Wu D, Malounda D, Nayak R, Kolios MC*. Pressure estimation of ultra-high frequency ultrasound using gas vesicles.<\/strong> Journal of the Acoustical Society of America<\/em> 156, 4193 (2024). article<\/a><\/p>\n

Han H#, Ma X#, Deng W#, Zhang J#, Tang S, Shun Pak o, Zhu L, Criado-Hidalgo E, Gong C, Karshalev E, Yoo J, You M, Liu A, Wang C, Shen HK, Patel PN, Hays CL, Gunnarson PJ, Li L, Zhang Y, Dabiri JO, Wang LV, Shapiro MG, Wu D*, Zhou Q*, Greer JR*, Gao W*. Imaging-guided bioresorbable acoustichydrogel microrobots<\/strong>. Science Robotics<\/em> 9, eadp3593 (2024). article<\/a><\/p>\n

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.<\/strong> ACS Synthetic Biology<\/em> 13, 2215 (2024). article<\/a><\/p>\n

Duan M#, Dev I#, Lu A, Ayrapetyan G, You MY, Shapiro MG*. SEMPER: Stoichiometric expression of mRNA polycistrons by eukaryotic ribosomes for compact, ratio-tunable multi-gene expression<\/strong>. Cell Systems<\/em> 15, 597 (2024). article<\/a><\/p>\n

Li H, Heath JE, Trippett JS, Shapiro MG*, Szablowski JO*. Engineering viral vectors for acoustically targeted gene delivery<\/strong>. Nature Communications<\/em> 15, 4924 (2024). article<\/a> <\/p>\n

\"\"Rabut C#, Norman S#*, Griggs W#, Russin JJ, Jann K, Christopoulos V, Liu C*, Andersen RA*, Shapiro MG*. Functional ultrasound imaging of human brain activity through an acoustically transparent cranial window<\/strong>. Science Translational Medicine<\/em> 16, eadj3143 (2024). article<\/a> | press<\/a><\/p>\n

Griggs WS*, Norman SL, Tanter M, Liu C, Christopoulos V, Shapiro M, Andersen RA. Functional ultrasound neuroimaging reveals mesoscopic organization of saccades in the lateral intraparietal area of posterior parietal cortex<\/strong>. bioRxiv preprint<\/a><\/p>\n

Nayak R, Duan M, Ling B, Jin Z, Malounda D, Shapiro MG*. Harmonic imaging for nonlinear detection of acoustic biomolecules<\/strong>. APL Bioengineering<\/em> 8, 046110 (2024). article<\/a><\/p>\n

\"\"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<\/strong>. Advanced Materials<\/em> 36, 2307106 (2024).
\narticle<\/a><\/p>\n

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<\/strong>. bioRxiv preprint<\/a><\/p>\n

\"\"Schrunk E, Dutka P, Hurt RC, Malounda D, Wi D*, Shapiro MG*. Bioorthogonal labeling enables in situ fluorescence imaging of expressed gas vesicle nanostructures<\/strong>. Bioconjugate Chemistry<\/em> 35, 333 (2024).
\narticle<\/a> <\/p>\n

Hou JF, Goni Nayeem MO, Caplan KA, Ruesch EA, Caban-Murillo A, Criado-Hidalgo E, Ornellas SB, Williams B, Pearce AA, Dagdeviren HE, Surets M, White JA, Shapiro MG, Wang F, Ramirez S, Dagdeviren C*. An implantable piezoelectric ultrasound stimulator (ImPULS) for deep brain activation<\/strong>. Nature Communications<\/em> 15, 4601 (2024). article<\/a> <\/p>\n

2023<\/span><\/span><\/strong><\/p>\n

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<\/strong>. Nature Neuroscience<\/em> (2023) article<\/a> | press<\/a><\/p>\n

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<\/strong>. Nano Letters<\/em> 23, 10748 (2023). article<\/a> <\/p>\n

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<\/strong>. iScience<\/em> 26, 108372 (2023). article<\/a> <\/p>\n

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<\/strong>. Nature Materials<\/em> (2023). article<\/a><\/p>\n

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<\/strong>. PNAS<\/em> 120, e2309822120 (2023). article<\/a> | press<\/a><\/p>\n

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<\/strong>. Structure<\/em> 31, 518 (2023) article<\/a><\/p>\n

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.<\/strong> Science Advances<\/em> 9, eadd9186 (2023). article<\/a> | press<\/a> | video<\/a><\/p>\n

\"\"<\/a>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<\/strong>. Nature Biotechnology<\/em> 41, 919 (2023). article<\/a> | research briefing<\/a><\/p>\n

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<\/strong>. Nature Electronics<\/em> 6, 242 (2023). article<\/a><\/p>\n

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<\/strong>. Brain Stimulation<\/em> 16, 604 (2023). article<\/a><\/p>\n

Xiong LL, Garrett MA, Kornfield JA*, Shapiro MG*. Living material with temperature-dependent light absorption<\/strong>. Advanced Science<\/em> 2301730 (2023) article<\/a><\/p>\n

Sharma S, Melton H, Edmonds L, Addington O, Shapiro MG, Emami A*. A monolithic 3D magnetic sensor in 65nm CMOS with <10\u03bcTrms noise and 14.8\u03bcW power<\/strong>. IEEE CICC<\/em> (2023). article<\/a><\/p>\n

2022<\/span><\/span><\/strong><\/p>\n

Salahshoor H#, Yao Y#, Dutka P#, Nystr\u00f6m NN, Jin Z, Min E, Malounda D, Jensen G, Ortiz M, Shapiro MG*. Geometric effects in gas vesicle buckling under ultrasound<\/strong>. Biophysical Journal<\/em> 121, 4221 (2022). article<\/a><\/p>\n

Xiong LL, Garrett MA, Buss MT, Kornfield JA, Shapiro MG*. Tunable temperature-sensitive transcriptional activation based on Lambda repressor<\/strong>. ACS Synthetic Biology<\/em> 11, 2518 (2022). article<\/a><\/p>\n

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<\/strong>. Nature Communications<\/em> 13, 1585 (2022). article<\/a><\/p>\n

Yoo S, Mittelstein DR, Hurt RC, Lacroix JJ, Shapiro MG*. Focused ultrasound excites cortical neurons via mechanosensitive calcium accumulation and ion channel amplification.<\/strong> Nature Communications<\/em> 13, 493 (2022). article<\/a> | readcube<\/a><\/p>\n

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.<\/strong> Nature<\/em> 602, 647 (2022). article<\/a><\/p>\n

Salahshoor H, Guo H, Shapiro MG, Ortiz M*. Mechanics of ultrasonic neuromodulation in a mouse subject<\/strong>. Extreme Mechanics Letters<\/em> 50, 101539 (2022). article<\/a><\/p>\n

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<\/strong>. Nature Communications<\/em> 13, 7311 (2022). article<\/a><\/p>\n

2021<\/span><\/span><\/strong><\/p>\n

Bar-Zion A*, Solomon O, Rabut C, Maresca D, Eldar YC, Shapiro MG. Doppler slicing for ultrasound super-resolution without contrast agents<\/strong>. bioRxiv preprint<\/a><\/p>\n

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<\/strong>. Nature Nanotechnology<\/em> 16, 1403\u20131412 (2021). article<\/a> | readcube<\/a><\/p>\n

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<\/strong>. Nature Methods<\/em> 18, 945-952 (2021). article<\/a> | readcube<\/a> | press<\/a><\/p>\n

Rabut C, Wu D, Ling B, Jin Z, Malounda D, Shapiro MG*. Ultrafast amplitude modulation for molecular and hemodynamic ultrasound imaging<\/strong>. Applied Physics Letters<\/em> 118, 244102 (2021). article<\/a> | bioRxiv preprint<\/a><\/p>\n

Yao Y, Jin Z, Ling B, Malounda D, Shapiro MG*. Self-assembly of protein superstructures by physical interactions under cytoplasm-like conditions<\/strong>. Biophysical Journal<\/em> 120, 2701-2709 (2021). article<\/a><\/p>\n

\"\"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<\/strong>. Neuron<\/em> 109, 1554-1566 (2021).
\narticle<\/a> | press<\/a> | bioRxiv preprint<\/a><\/p>\n

\"\"Buss MT#, Ramesh P#, English MA, Lee-Gosselin A, Shapiro MG*. Spatial control of probiotic bacteria in the gastrointestinal tract assisted by magnetic particles<\/strong>. Advanced Materials<\/em> 33, 2007473 (2021).
\narticle<\/a><\/p>\n

Farhadi A, Sigmund F, Westmeyer GG*, Shapiro MG*. Genetically encodable materials for non-invasive biological imaging<\/strong>. Nature Materials<\/em> 20, 585-592 (2021). article<\/a> | readcube<\/a><\/p>\n

Sharma S*, Telikicherla A; Ding G; Aghlmand F; Hashemi Talkhooncheh A; Shapiro MG, Emami A. Wireless 3D surgical navigation and tracking system with 100 \u00b5m accuracy using magnetic-field gradient-based localization<\/strong>. IEEE Transactions on Medical Imaging<\/em> (2021). article<\/a><\/p>\n

Dutka P, Malounda D, Metskas LA, Chen S, Hurt RC, Lu GJ, Jensen GJ*, Shapiro MG*. Measuring gas vesicle dimensions by electron microscopy<\/strong>. Protein Science<\/em> 30, 1081-86 (2021). article<\/a> | bioRxiv preprint<\/a><\/p>\n

2020<\/span><\/span><\/strong><\/p>\n

Rabut C, Yoo S, Hurt RC, Jin Z, Guo H, Ling B, Shapiro MG*. Ultrasound technologies for imaging and modulating neural activity.<\/strong> Neuron<\/em> 108, 93-110 (2020). article<\/a><\/p>\n

Ling B, Lee J, Maresca D, Lee-Gosselin A, Malounda D, Swift MB, Shapiro MG*. Biomolecular ultrasound imaging of phagolysosomal function.<\/strong> ACS Nano<\/em> 14, 12210-12221 (2020). article<\/a><\/p>\n

Abedi MH, Lee J, Piraner DI, Shapiro MG*. Thermal control of engineered T-cells.<\/strong> ACS Synthetic Biology<\/em> 9, 1941-50 (2020). article<\/a> | bioRxiv preprint<\/a><\/p>\n

\"\"<\/a>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.<\/strong> Nature Chemical Biology<\/em> 16, 988-96 (2020).
\narticle<\/a> | readcube<\/a> | behind the paper<\/a> | press<\/a><\/p>\n

Salahshoor H*, Shapiro MG*, Ortiz M*. Transcranial focused ultrasound generates skull-conducted shear waves: computational model and implications for neuromodulation.<\/strong> Applied Physics Letters<\/em> 117, 033702 (2020). article<\/a> | bioRxiv preprint<\/a><\/p>\n

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.<\/strong> Biophysical Journal<\/em> 118, 1502-1510 (2020). article<\/a><\/p>\n

Farhadi A#, Bedrossian M#, Lee J, Ho GH, Shapiro MG*, Nadeau J*. Genetically encoded phase contrast agents for digital holographic microscopy.<\/strong> Nano Letters<\/em> (2020). article<\/a><\/p>\n

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.<\/strong> Proceedings of the Royal Society A<\/em> 476, 20190692 (2020). article<\/a><\/p>\n

Zhang S#, Huang A#, Bar\u2010Zion A, Wang J, Vazquez Mena O, Shapiro MG, Friend J*. The vibration behavior of sub\u2010micrometer gas vesicles in response to acoustic excitation determined via laser doppler vibrometry.<\/strong> Advanced Functional Materials<\/em> 2020, 2000239 (2020). article<\/a><\/p>\n

Lu GJ, Chou L, Malounda D, Patel AK, Welsbie DS, Chou DL*, Ramalingam T*, Shapiro MG*. Genetically encodable contrast agents for optical coherence tomography.<\/strong> ACS Nano<\/em> 14, 7, 7823-7831 (2020). article<\/a> | bioRxiv preprint<\/a><\/p>\n

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.<\/strong> Applied Physics Letters<\/em> 116, 013701 (2020). article<\/a><\/p>\n

2019<\/span><\/span><\/strong><\/p>\n

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.<\/strong> NeuroImage<\/em> 209, 116467 (2019). article<\/a><\/p>\n

Farhadi A, Ho GH, Sawyer DP, Bourdeau RW, Shapiro MG*. Ultrasound imaging of gene expression in mammalian cells.<\/strong> Science<\/em> 365, 1469-1475 (2019). article<\/a> | perspective<\/a> | press<\/a><\/p>\n

Piraner DI, Wu Y, Shapiro MG*. Modular thermal control of protein dimerization.<\/strong> ACS Synthetic Biology<\/em> 8, 2256-2262 (2019). article<\/a><\/p>\n

Szablowski JO#, Bar-Zion A#, Shapiro MG*. Achieving spatial and molecular specificity with ultrasound-targeted biomolecular nanotherapeutics.<\/strong> Accounts of Chemical Research<\/em> 52, 2427 – 2434 (2019). article<\/a><\/p>\n

2018<\/span><\/span><\/strong><\/p>\n

Maresca D#*, Sawyer DP#, Renaud G, Lee-Gosselin A, Shapiro MG*. Nonlinear X-wave ultrasound imaging of acoustic biomolecules.<\/strong> Physical Review X<\/em> 8, 041002 (2018).
\narticle<\/a> | synopsis<\/a><\/p>\n

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.<\/strong> Angewandte Chemie<\/em> 57, 12385-12389 (2018). article<\/a><\/p>\n

Kunth M, Lu GJ, Witte C, Shapiro MG*, Schr\u00f6der L*. Protein nanostructures produce self-adjusting hyperpolarized magnetic resonance imaging contrast through physical gas partitioning.<\/strong> ACS Nano<\/em> 12, 10939-10948 (2018). article<\/a><\/p>\n

\"\"<\/a>Szablowski JO, Lue B, Lee-Gosselin A, Malounda D, Shapiro MG*. Acoustically targeted chemogenetics for the non-invasive control of neural circuits.<\/strong>
\nNature Biomedical Engineering <\/em> 2, 475-484 (2018).
\narticle<\/a> | readcube<\/a> | news and views<\/a> | press<\/a> | behind the paper<\/a><\/p>\n

Sato T*, Shapiro MG#*, Tsao DY#*. Ultrasonic neuromodulation causes widespread cortical activation via an indirect auditory mechanism.<\/strong> Neuron <\/em>98, 1031-1041 (2018). article<\/a> | companion article<\/a><\/p>\n

\"\"<\/a>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.<\/strong> Nature Materials<\/em> 17, 456\u2013463 (2018).
\narticle<\/a> | readcube<\/a> | news and views<\/a> | press<\/a> | behind the paper<\/a><\/p>\n

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.<\/strong> Annual Review of Chemical and Biomolecular Engineering<\/em> 9, 229-252 (2018). article<\/a><\/p>\n

Lu GJ#, Farhadi A#, Mukherjee A, Shapiro MG*. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging.<\/strong> Current Opinion in Chemical Biology<\/em> 45, 57-63 (2018). article<\/a><\/p>\n

Farhadi A, Ho G, Kunth M, Ling B, Lakshmanan A, Lu GJ, Bourdeau RW, Schr\u00f6der L, Shapiro MG*.  Recombinantly expressed gas vesicles as nanoscale contrast agents for ultrasound and hyperpolarized MRI.<\/strong> AIChE Journal<\/em> 64, 2927-2933 (2018). article<\/a><\/p>\n

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.<\/strong> Nature Communications <\/em> 9, 131 (2018). article<\/a> | press<\/a><\/p>\n

\"\"<\/a>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.<\/strong> Nature <\/em> 553, 86\u201390 (2018).
\narticle<\/a> | readcube<\/a> | news and views<\/a> | press<\/a> | behind the paper<\/a><\/p>\n

Le Floc\u2019h 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. <\/strong> Molecular Imaging and Biology<\/em> 20, 230-239 (2018). article<\/a><\/p>\n

2017<\/span><\/span><\/strong><\/p>\n

\"\"<\/a>Monge M, Lee-Gosselin A, Shapiro MG*, Emami A*. Localization of microscale devices in vivo using addressable transmitters operated as magnetic spins.<\/strong> Nature Biomedical Engineering <\/em> 1, 736-744 (2017).
\narticle<\/a> | readcube<\/a> | news and views<\/a> | press<\/a> | behind the paper<\/a><\/p>\n

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, Schr\u00f6der L, Shapiro MG*. Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI. <\/strong> Nature Protocols <\/em> 12, 2050-2080 (2017). article<\/a> | readcube<\/a><\/p>\n

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.<\/strong> Biochemistry <\/em> (2017). article<\/a><\/p>\n

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.<\/strong> Molecular Therapy <\/em> 26, 304-319 (2017). article<\/a><\/p>\n

Maley AM, Lu GJ, Shapiro MG, Corn RM*. Characterizing single polymeric and protein nanoparticles with surface plasmon resonance imaging measurements.<\/strong> ACS Nano<\/em> 11, 7447-7456 (2017). article<\/a><\/p>\n

Mukherjee A, Davis HC, Ramesh P, Lu GJ, Shapiro MG*. Biomolecular MRI reporters: evolution of new mechanisms.<\/strong> Progress in NMR Spectroscopy<\/em> 102-103, 32-42 (2017). <\/em> article<\/a><\/p>\n

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.<\/strong> Ultrasound in Medicine and Biology <\/em>43, 1016-1030 (2017). article<\/a><\/p>\n

Maresca D, Lakshmanan A, Lee-Gosselin A, Melis JM, Ni YL, Bourdeau RW, Kochmann DM, Shapiro MG*. Nonlinear ultrasound imaging of nanoscale acoustic biomolecules.<\/strong> Applied Physics Letters <\/em>110, 073704 (2017). article<\/a><\/p>\n

Gilad AA*, Shapiro MG*. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.<\/strong> Molecular Imaging and Biology <\/em>19, 373-378 (2017). article<\/a><\/p>\n

Piraner DI#, Abedi MH#, Moser BA, Lee-Gosselin A, Shapiro MG*. Tunable thermal bioswitches for in vivo control of microbial therapeutics. <\/strong>Nature Chemical Biology <\/em>13, 75-80 (2017). article<\/a> | press<\/a> | video<\/a> | highlight in Nature Methods<\/a><\/p>\n

2016<\/span><\/span><\/strong><\/p>\n

Mukherjee A#, Wu D#, Davis HC, Shapiro MG*. Noninvasive imaging using reporter genes altering cellular water permeability.<\/strong> Nature Communications <\/em>7, 13891 (2016). article<\/a> | press<\/a> | highlight in Lab Animal<\/a><\/p>\n

\"\"<\/a>Barksiy DA, Goodson BM, Branca RT, Lu GJ, Shapiro MG, Schr\u00f6der L, Chekmenev EY*, et al. NMR hyperpolarization techniques of gases. <\/strong>Chemistry\u2013A European Journal<\/em> 23, 725-751 (2016).
\narticle<\/a><\/p>\n

\"\"<\/a>Lakshmanan A, Farhadi A, Nety SP, Lee-Gosselin A, Bourdeau RW, Maresca D, Shapiro MG*. Molecular engineering of acoustic protein nanostructures.<\/strong> ACS Nano<\/em> 10, 7314-22 (2016).
\narticle<\/a> | press<\/a><\/p>\n

2014<\/span><\/span><\/strong><\/p>\n

Shapiro MG*, Ramirez RM, Sperling LJ, Sun G, Pines A, Schaffer DV, Bajaj VS*. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. <\/strong> Nature Chemistry<\/em> 6, 629-34 (2014). article<\/a> | commentary in Science Translational Medicine<\/a><\/p>\n

Shapiro MG*, Goodwill PW, Neogy A, Yin M, Foster FS, Schaffer DV, Conolly SM. Biogenic gas nanostructures as ultrasonic molecular reporters. <\/strong> Nature Nanotechnology <\/em>9, 311-6 (2014). article<\/a> | news and views<\/a><\/p>\n

2013 and earlier<\/span><\/span><\/strong><\/p>\n

Marblestone AH, Zamft BM, Shapiro MG, Boyden ES, Church GM, Kording KP, et al. Physical Principles for Scalable Neural Recording.<\/strong> Frontiers in Computational Neuroscience<\/em> (2013). article<\/a><\/p>\n

Shapiro MG*, Priest MF, Siegel PH, Bezanilla F*. Thermal mechanisms of millimeter wave stimulation of excitable cells. <\/strong> Biophysical Journal<\/em> (2013). article<\/a><\/p>\n

Romero PA, Shapiro MG, Arnold FH, Jasanoff A. Directed evolution of protein-based neurotransmitter sensors for MRI.<\/strong><\/span> Methods in Molecular Biology<\/em> 995, 193-205 (2013). article<\/a><\/p>\n

Shapiro MG*, Frazier SJ, Lester HA. Unparalleled control of neural activity using orthogonal pharmacogenetics. <\/strong> ACS Chemical Neuroscience<\/em> (2012). article<\/a><\/p>\n

Shapiro MG, Homma K, Villarreal S, Richter CP, Bezanilla F. Infrared light excites cells by changing their electrical capacitance.<\/strong><\/span> Nature Communications<\/em> 3:736 (2012). article<\/a><\/p>\n

Shapiro MG, Westmeyer GG, Romero PA, Szablowski JO, K\u00fcster 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.<\/strong> Nature Biotechnology<\/em> 28, 264-70 (2010). article<\/a><\/p>\n

Shapiro MG, Szablowsky JO, Langer R, Jasanoff A. Protein nanoparticles engineered to sense kinase activity in MRI. <\/strong> Journal of the American Chemical Society<\/em> 131, 2484-6 (2009). article<\/a><\/p>\n

Shapiro MG, Atanasijevich T, Faas H, Westmeyer GG, Jasanoff A. Dynamic imaging with MRI contrast agents: quantitative considerations.<\/strong> Magnetic Resonance Imaging<\/em> 24, 449-62 (2006). article<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

(#equal contribution, *corresponding) 2025 Nystr\u00f6m NN, Jin Z, Bennett ME, Zhang R, Swift MB, Shapiro MG*. Multiplexed ultrasound imaging of gene expression. Nature Methods (2025). article Schrunk E, Lee S, …<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-23","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/pages\/23","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=23"}],"version-history":[{"count":318,"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/pages\/23\/revisions"}],"predecessor-version":[{"id":2028,"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=\/wp\/v2\/pages\/23\/revisions\/2028"}],"wp:attachment":[{"href":"https:\/\/shapirolab.caltech.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}