Publications

Full publication archive from the Di Carlo Lab.

Selected Recent Publications

Nature Protocols (2025)

Linking single-cell transcriptomes with secretion using SEC-seq

Langerman J, Baghdasarian S, Cheng RYH, James RG, Plath K, Di Carlo D

Nature Nanotechnology (2024)

Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq

Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Di Carlo D

Nature Communications (2024)

Optimizing cell therapy by sorting cells with high extracellular vesicle secretion

Koo D, Chen X, Udani S, Baghdasarian S, Zhu D, Li J, Hall B, Tsubamoto N, Hu S, Ko J, Cheng K, Di Carlo D

Nature Communications (2024)

Rapid single-tier serodiagnosis of Lyme disease

Ghosh R, Joung HA, Goncharov A, Palanisamy B, Ozcan A, Garner O, Di Carlo D, and collaborators

PNAS (2024)

Defining T cell receptor repertoires using nanovial-based binding and functional screening

Koo D, Mao Z, Dimatteo R, Noguchi M, Tsubamoto N, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Burton Sojo G, Witte O, Di Carlo D

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Nature Biotechnology (2026)

Mapping and engineering the human cell-cell interactome

Di Carlo D, Morsut L, McCain ML, Wright HJ, Abedi M, Yamada-Hunter SA, Zhang JZ, Backus K, Chung E, Wang Y, Rando TA, Cai L, Thomson M, Elowitz MB, Lee JK, Witte O

bioRxiv (2026)

Lab-on-a-3D-Printer for Democratized Reconfigurable Digital Microfluidics

Ye S, Schremmer BR, Guan Z, Goncharov A, Han GR, Rajasenan V, Falcone N, Li X, McDonough CR, Ozcan A, Di Carlo D

Nature Protocols (2025)

Linking single-cell transcriptomes with secretion using SEC-seq

Langerman J, Baghdasarian S, Cheng RYH, James RG, Plath K, Di Carlo D

Nature Communications (2024)

Rapid single-tier serodiagnosis of Lyme disease

Ghosh R, Joung HA, Goncharov A, Palanisamy B, Ozcan A, Garner O, Di Carlo D, and collaborators

Nature Communications (2024)

Optimizing cell therapy by sorting cells with high extracellular vesicle secretion

Koo D, Chen X, Udani S, Baghdasarian S, Zhu D, Li J, Hall B, Tsubamoto N, Hu S, Ko J, Cheng K, Di Carlo D

ACS (2024)

Lab on a Particle Technologies

Ghosh R, Arnheim A, van Zee M, Shang L, Soemardy C, Tang R, Mellody M, Baghdasarian S, Sanchez Ochoa E, Ye S, Chen S, Williamson C, Karunaratne A, Di Carlo D

PNAS (2024)

Defining T cell receptor repertoires using nanovial-based binding and functional screening

Koo D, Mao Z, Dimatteo R, Noguchi M, Tsubamoto N, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Burton Sojo G, Witte O, Di Carlo D

Nature Nanotechnology (2024)

Associating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seq

Udani S, Langerman J, Koo D, Baghdasarian S, Cheng B, Kang S, Soemardy C, de Rutte J, Plath K, Di Carlo D

Advanced Science (2023)

Improved humoral immunity and protection against influenza virus infection with a 3d porous biomaterial vaccine

Miwa H, Antao OQ, Kelly-Scumpia KM, Baghdasarian S, Mayer D, Shang L, Sanchez GM, Archang MM, Scumpia PO, Weinstein JS, Di Carlo D

Med-X (2023)

Fluorescence imaging deformability cytometry: integrating nuclear structure with mechanical phenotyping

Muñoz HE, Lin J, Yeh BG, Biswas T, Di Carlo D

Nature Communications (2023)

SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells

Cheng R, de Rutte J, Ito C, Ott A, Bosler L, Kuo WY, Liang J, Hall B, Rawlings D, Di Carlo D, James R

Nature (2022)

Ferrobotic swarms enable accessible and adaptable automated viral testing

Lin H, Yu W, Sabet K, Bogumil M, Zhao Y, Hambalek J, Lin S, Chandrasekaran S, Garner O, Di Carlo D & Emaminejad S

Ferrobotic swarms enable accessible and adaptable automated viral testing

Life (2022)

Enabling clonal analyses of yeast in outer space by encapsulation and desiccation in hollow microparticles

Ng Simon, Williamson C, van Zee M, Di Carlo D, Santa Maria SR

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ACS Nano (2022)

Suspendable hydrogel nanovials for massively parallel single-cell functional analysis and sorting

de Rutte J, Dimatteo R, Archang M, van Zee M, Koo D, Lee S, Sharrow A, Krohl P, Mellody M, Zhu S, Eichenbaum J, Kizerwetter M, Udani S, Ha K, Willson R, Bertozzi A, Spangler J, Damoiseaux R, Di Carlo D

Lab on a Chip (2022)

IL-2 secretion-based sorting of single T cells using high-throughput microfluidic on-cell cytokine capture

Dimatteo R and Di Carlo D

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PNAS (2022)

High-throughput selection of cells based on accumulated growth and division using PicoShell particles

van Zee M, de Rutte J, Rumyan R, Williamson C, Burnes T, Radakovits R, Eugenio A, Badih S, Lee S, Lee DH, Archang M, Di Carlo D

ACS Nano (2021)

Scalable fabrication and use of 3D structured microparticles spatially functionalized with biomolecules

Lee S, de Rutte J, Dimatteo R, Koo D, Di Carlo D

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ACS Sensors (2021)

Methylation-sensitive loop-mediated isothermal amplification (LAMP): nucleic acid methylation detection through LAMP with mobile fluorescence readout

Hambalek J, Kong J, Brown C, Munoz HE, Horn T, Bogumil M, Quick E, Ozcan A, Di Carlo D

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Lab on a Chip (2021)

Counting of enzymatically amplified affinity reactions in hydrogel particle-templated drops

Wang Y, Shah V, Lu A, Pachler E, Cheng B, Di Carlo D

Physical Review E (2021)

Statistical energy minimization theory for systems of drop-carrier particles

Du R, Liu L, Ng S, Sambandam S, Adame B, Perez H, Ha K, Falcon C, de Rutte J, Di Carlo D, Bertozzi A

Advanced Materials (2021)

Single-domain multiferroic array-addressable terfenol-D (SMArt) micromagnets for programmable single-cell capture and release

Khojah R, Xiao Z, Panduranga M, Bogumil M, Wang Y, Goiriena-Goikoetxea M, Chopdekar R, Bokar J, Carman G, Candler R, Di Carlo D

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PLoS ONE (2021)

Magnetic microparticle concentration and collection using a mechatronic magnetic ratcheting system

Adeyiga O, Murray C, Muñoz HE, Escobar A, Di Carlo D

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Analytical Chemistry (2021)

Engineering design of concentric amphiphilic microparticles for spontaneous formation of picoliter to nanoliter droplet volumes

Destgeer G, Ouyang M, Di Carlo D

Optics Express (2020)

Scanning two-photon continuous flow lithography for the fabrication of multi-functional microparticles

Chizari S, Udani S, Farzaneh A, Stoecklein D, Di Carlo D, Hopkins J

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Biosensors and Bioelectronics (2020)

A review of biosensor technologies for blood biomarkers toward monitoring cardiovascular disease at the point-of-care

Ouyang M, Tu D, Tong L, Sarwar M, Bhimaraj A, Li C, Cote G, Di Carlo D

Science Advances (2020)

Monodisperse drops templated by 3D-structured microparticles

Wu CY, Ouyang M, Wang B, de Rutte J, Joo A, Jacobs, M, Ha K, Bertozzi A, Di Carlo D

Monodisperse drops templated by 3D-structured microparticles

Nature Materials (2020)

Activating an adaptive immune response from a hydrogel scaffold imparts regenerative wound healing

Griffin D, Archang M, Kuan CH, Weaver W, Weinstein J, Feng AC, Ruccia A, Sideris E, Ragkousis V, Koh J, Plikus M, Di Carlo D, Segura T, Scumpia P

Activating an adaptive immune response from a hydrogel scaffold imparts regenerative wound healing

Advanced Functional Materials (2020)

Injectable drug‐releasing microporous annealed particle scaffolds for treating myocardial infarction

Fang J, Koh J, Fang Q, Qui H, Archang M, Hasani-Sadrabadi M, Miwa H, Zhong X, Sievers R, Gao D, Lee R, Di Carlo D, Li S

Journal of Neuroscience Methods (2020)

Peripheral focused ultrasound neuromodulation (pFUS)

Cotero V, Miwa H, Graf J, Ashe J, Loghin E, Di Carlo D, Puleo C

Nature Methods (2020)

A comparison of microfluidic methods for high-throughput cell deformability measurements

Muñoz HE, Urbanska M, Bagnall JS, Otto O, Manalis SR, Di Carlo D, Guck J.

Nature Communications (2020)

Spectro-temporal encoded multiphoton microscopy and fluorescence lifetime imagaing at kilohertz frame-rates

Karpf S, Riche CT, Di Carlo D, Goel A, Zeiger WA, Suresh A, Portera-Cailliau C, Jalali B

Lab on a Chip (2020)

Fabrication of 3D concentric amphiphilic microparticles to form uniform nanoliter reaction volumes for amplified affinity assays

Destgeer G, Ouyang M, Wu CY, Di Carlo D

Science Robotics (2020)

A ferrobotic system for automated microfluidic logistics

Yu W, Lin H, Wang Y, He X, Chen N, Sun K, Lo D, Cheng B, Yeung C, Tan J, Di Carlo D, Emaminejad S

ACS Sensors (2020)

Fractal LAMP: Label-free analysis of fractal precipitate for digital loop-mediated isothermal nucleic acid amplification

Munoz HE, Riche CT, Kong JE, van Zee M, Garner OB, Ozcan A, and Di Carlo D

Light: Science & Applications (2019)

Computational cytometer based on magnetically modulated coherent imaging and deep learning

Zhang Y, Ouyang M, Ray A, Liu T, Kong J, Bai B, Kim D, Guziak A, Luo Y, Feizi A, Tsai K, Duan Z, Liu X, Kim D, Cheung C, Yalcin S, Koydemir H, Garner O, Di Carlo D, Ozcan A

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Small (2019)

Enhanced in vivo delivery of stem cells using microporous annealed particle scaffolds

Koh J, Griffin DR, Archang MM, Feng A, Horn T, Margolis M, Zalazar D, Segura T, Scumpia P, Di Carlo D

Advanced Functional Materials (2019)

Scalable high-throughput production of modular microgels for in situ assembly of microporous tissue scaffolds

de Rutte J, Koh J, and Di Carlo D

Biosensors and Bioelectronics (2019)

Nanoplasmonic swarm biosensing using single nanoparticle colorimetery

Ouyang M and Di Carlo D

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Analytical Chemistry (2019)

Review: Nonlinear Microfluidics

Stoecklein D and Di Carlo D

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Microsystems and Nanoengineering (2018)

Shaped 3D microcarriers for adherent cell culture and analysis

Wu CY, Stoecklein D, Kommajosula, Lin J, Owsley K, Ganapathysubramanian B, Di Carlo D

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Applied and Environmental Microbiology (2018)

High-throughput microfluidic sorting of live magnetotactic bacteria

Tay A, Pfeiffer D, Rowe K, Tannabaum A, Popp F, Strangeway R, Schuler D, and Di Carlo D

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Small (2018)

A gelatin microdroplet platform for high-throughput sorting of hyperproducing single-cell derived microalgal clones

Li M, van Zee M, Riche C, Tofig B, Gallaher S, Merchant S, Damoiseaux R, Goda K, Di Carlo D

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PNAS (2018)

Functional profiling of circulating tumor cells with an integrated vortex capture and single-cell protease activity

Dhar M, Lam JN, Walser T, Dubinett SM, Rettig MB, and Di Carlo D

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Analytical Chemistry (2018)

Single-cell analysis of morphological and metabolic heterogeneity in Euglena gracilis by fluorescence-imaging flow cytometry

Munoz HE, Li M, Riche CT, Nitta N, Diebold E, Lin J, Owsley K, Bahr M, Goda K, and Di Carlo D

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Lab on a Chip (2018)

Size-based sorting of hydrogel droplets using inertial microfluidics

Li M, van Zee M, Goda K, and Di Carlo D

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Lab on a Chip (2018)

Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting

Murray C, Miwa H, Dhar M, Park D, Pao E, Martinez J, Kaanumale E, Graf Rhaddasi K, Kwok W, Hafler D, Puleo C, and Di Carlo D

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Analytical Chemistry (2018)

Ferrodrop dose-optimized digital quantification of biomolecules in low-volume samples

Kahkeshani S, Kong J, Wei Q, Tseng D, Garner O, Ozcan A, and Di Carlo D

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Advanced Materials (2018)

Hyaluronic acid hydrogel for magnetomechanical neuromodulation of primary root ganglion neurons

Tay A, Sohrabi A, Poole K, Seidlits S, and Di Carlo D

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Scientific Reports (2018)

Evaluation of PD-L1expression on vortex-isolated circulating tumor cells in metastatic lung cancer

Dhar M, Wong J, Che J, Matsumoto M, Grogan T, Elashoff D, Garon EB, Goldman JW, Sollier Christen E, Di Carlo D, and Kelkarni RP

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Biomicrofluidics (2018)

Separation of cancer cells using vortical microfluidic flows

Haddadi H, Naghsh-Nilchi H, and Di Carlo D

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Analytical Chemistry (2017)

Enzyme-free nucleic acid amplification assay using a cellphone based well plate fluorescence reader

Kim D, Wei Q, Kim DH, Tseng D, Zhang J, Pan E, Garner O, Ozcan A, and Di Carlo D

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Advanced Functional Materials (2017)

Phenotypic selection of Magnetospirillum magneticum (AMB-1) overproducers using magnetic ratcheting

Tay A, Murray C, and Di Carlo D

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Biophysical Journal (2017)

Probing cell adhesion profiles with a microscale adhesive choice assay

Kittur H, Tay A, Hua A, Yu M, and Di Carlo D

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SLAS TECHNOLOGY: Translating Life Sciences Innovation (2017)

Continuous and quantitative purification of T-cell subsets for cell therapy manufacturing using magnetic ratcheting cytometry

Murray C, Pao E, Jann A, Park DE, and Di Carlo D

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Microfluidics and Nanofluidics (2017)

Effect of reservoir geometry on vortex trapping of cancer cells

Che J, and Di Carlo D

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Lab on a Chip (2017)

Size-tunable microvortex capture of rare cells

Khojah R, Stoutamore R, and Di Carlo D

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Lab on a Chip (2017)

Biophysical isolation and identification of circulating tumor cells

Che J, Yu V, Garon EB, Goldman JW, and Di Carlo D

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Lab on a Chip (2017)

Modulating motility of intracellular vesicles in cortical neurons with nanomagnetic forces on-chip

Kunze A, Murray C, Godzich C, Lin J, Owsley K, Tay A, and Di Carlo D

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Scientific Reports (2017)

Shape-based separation of microalga Euglena gracilis

Li M, Munoz HE, Goda K, and Di Carlo D

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Microsystems and Nanoengineering (2017)

High-throughput physical phenotyping of cell differentiation

Lin J, Kim D, Tse HT, Tseng P, Peng L, Dhar M, Karumbayaram K, and Di Carlo D

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Lab on a Chip (2017)

Inertial focusing of ellipsoidal Euglena gracilis cells in a stepped microchannel

Li M, Munoz HE, Schmidt A, Guo B, Lei C, Goda K, and Di Carlo D

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Nature Biomedical Engineering (2017)

Elastomeric sensor surfaces for high-throughput single-cell force cytometry

Pushkarsky I, Tseng P, Black D, France B, Warfe L, Koziol-White C, Jester W, Trinh R, Lin J, Sumpia P, Morrison S, Panettieri R, Damoiseaux R, and Di Carlo D

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ACS Nano (2017)

Highly stable and sensitive nucleic acid amplification and cellphone based readout

Kong J, Wei Q, Tseng D, Zheng J, Pan E, Lewinski M, Garner OB, Ozcan A, and Di Carlo D

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Nano Letters (2017)

Magnetic nanoparticle-based mechanical stimulation for restoration of mechano-sensitive ion channel equilibrium in neural networks

Tay A and Di Carlo D

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Journal of Fluid Mechanics (2017)

Inertial flow of a dilute suspension over cavities in a microchannel

Haddadi H and Di Carlo D

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Journal of Current Medical Chemistry (2016)

Remote neural stimulation using magnetic nanoparticles

Tay A and Di Carlo D

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Scientific Reports (2016)

Label-free enumeration, collection, and downstream cytological and cytogenic analysis of circulating tumor cells

Dhar M, Pao E, Renier C, Go DE, Che J, Montoya R, Conrad R, Matsumoto M, Heirich K, Triboulet M, Rao J, Jeffrey SS, Garon EB, Goldman J, Rao NP, Kulkarni R, Sollier-Christen E, and Di Carlo D

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ACS Nano (2016)

Homogeneous entropy-driven amplified detection of biomolecular interactions

Kim D, Garner OB, Ozcan A, and Di Carlo D

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Scientific Reports (2016)

Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping

Sung K, Ding Y, Ma J, Chen H, Huang V, cheng M, Yang CF, Kim JT, Eguchi D, Di Carlo D, Hsiai TK, Nakano, and Kulkarni RP

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Lab on a Chip (2016)

Direct measurement of particle inertial migration in rectangular microchannels

Hood K, Kahkeshani S, Di Carlo D, and Roper M

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Small (2016)

The age of cortical neural networks affects their interactions with magnetic nanoparticles

Tay A, Kunze A, Jun D, Hoek E, and Di Carlo D

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Lab on a Chip (2016)

Drop formation using ferrofluids driven magnetically in a step emulsification device

Kahkeshani S and Di Carlo D

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Lab on a Chip (2016)

Micro- and nano-technologies to probe the mechano-biology of the brain

Tay A, Schweizer FE, and Di Carlo D

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Small (2016)

Quantitative magnetic separation of particles and cells using gradient magnetic ratcheting

Murray C, Pao E, Tseng P, Aftab S, Kulkarni R, Retti M, Di Carlo D

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ACS Nano (2016)

Induction of calcium influx in cortical neural networks by nanomagnetic forces

Tay A, Kunze A, Murray C, and Di Carlo D

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Oncotarget (2016)

Classification of large circulating tumor cells isolated with ultra-high throughput microfluidic Vortex technology

Che J, Yu V, Dhar M, Renier C, Matsumoto M, Heirich K, Garon EB, Goldman J, Rao J, Sledge GW, Pegram MD, Sheth S, Jeffrey SS, Kulkarni K, Sollier E, and Di Carlo D

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Biomicrofluidics (2015)

High efficiency vortex trapping of circulating tumor cells

Dhar M, Wong J, Karimi A, Che, J, Renier C, Matsumoto M, Triboulet T, Garon EB, Goldman JW, Rettig MB, Jeffrey SS, Kulkarni RP, Sollier E, and Di Carlo D