Research & Publications

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Publications by Our Users

This page contains some research and publications resulting from work carried out by HMS Microfluidics users with the utilization of the HMS microfabrication/microfluidics Core facility:

* Laser Speckle Rheology for evaluating the viscoelastic properties of hydrogel scaffolds. Zeinab Hajjarian, Hadi Tavakoli Nia, Shawn Ahn, Alan J. Grodzonsky, Rakesh K. Jain & Seemantini K. Nadkarni. Nature Publishing Group. http://dx.doi.org/10.1038/srep37949

* Uptake of rabies virus into epithelial cells by clathrin-mediated endocytosis depends upon actin. Piccinotti S, Kirchhausen T, Whelan SP. J Virol. 2013 Nov;87(21):11637-47. doi: 10.1128/JVI.01648-13

* Memory and Modularity in Cell-Fate Decision Making. Thomas M. Norman, Nathan D. lord, Johan Paulsson,Richard Losick. (Nature. Nov 28, 2013; 503(7477): 481–486.)

* Absolute quantification of protein copy number using a single-molecule-sensitive microarray. Burgin E, Salehi-Reyhani A, Barclay M, Brown A, Kaplinsky J, Novakova M, Neil MA, Ces O, Willison KR, Klug DR

* Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro. Torisawa YS, Spina CS, Mammoto T, Mammoto A, Weaver JC, Tat T, Collins JJ, Ingber DE.

* Microengineered physiological biomimicry: Organs-on-Chips. Dongeun Huh, Yu-suke Torisawa, Geraldine A. Hamilton, Hyun Jung Kima and Donald E. Ingber

*Screening therapeutic EMT blocking agents in a three-dimensional microenvironment. Aref AR, Huang RY, Yu WA Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I., Chua KN, Sun W, Tu TY, Bai J, Sim WJ, Zervantonakis IK, Thiery JP, Kamm RD.1.Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Evan Z. Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R. Bialas, Nolan Kamitaki, Emily M. Martersteck, John J. Trombetta, David A. Weitz, 10, Joshua R. Sanes, Alex K. Shalek, Aviv Regev, Steven A. McCarroll.

* An extracorporeal blood-cleansing device for sepsis therapy. Kang JH, Super M, Yung CW, Cooper RM, Domansky K, Graveline AR, Mammoto T, Berthet JB, Tobin H, Cartwright MJ, Watters AL, Rottman M, Waterhouse A, Mammoto A, Gamini N, Rodas MJ, Kole A, Jiang A, Valentin TM, Diaz A, Takahashi K, Ingber DE.

* Development of covalent inhibitors that can overcome resistance to first-generation FGFR kinase inhibitors. Tan L, Wang J, Tanizaki J, Huang Z, Aref AR, Rusan M, Zhu SJ, Zhang Y, Ercan D, Liao RG, Capelletti M, Zhou W, Hur W, Kim N, Sim T, Gaudet S, Barbie DA, Yeh JR, Yun CH, Hammerman PS, Mohammadi M, Jänne PA, Gray NS.

* Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC, Reibel JB, Tamayo P, Godfrey JT, Qian ZR, Page AN, Maciag K, Chan EM, Silkworth W, Labowsky MT, Rozhansky L, Mesirov JP, Gillanders WE, Ogino S, Hacohen N, Gaudet S, Eck MJ, Engelman JA, Corcoran RB, Wong KK, Hahn WC, Barbie DA.

* Complementary effects of ciclopirox olamine, a prolyl hydroxylase inhibitor and sphingosine 1-phosphate on fibroblasts and endothelial cells in driving capillary sprouting. Sei Hien Lim,  Choong Kim,  Amir R. Aref, Roger D. Kamm and Michael Raghunath.

* Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells. Allon M. Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A. Weitz, Marc W. Kirschner.

* Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Evan Z. Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R. Bialas, Nolan Kamitaki, Emily M. Martersteck, John J. Trombetta, David A. Weitz, 10, Joshua R. Sanes, Alex K. Shalek, Aviv Regev, Steven A. McCarroll.

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M.

* A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I.

* Microfluidic systems for stem cell-based neural tissue engineering. Karimi M, Bahrami S, Mirshekari H, Basri SM, Nik AB, Aref AR, Akbari M, Hamblin MR. Lab Chip. 2016 Jul 5;16(14):2551-71. doi: 10.1039/c6lc00489j.

* Engineered in vitro disease models. Benam KH, Dauth S, Hassell B, Herland A, Jain A, Jang KJ, Karalis K, Kim HJ, MacQueen L, Mahmoodian R, Musah S, Torisawa YS, van der Meer AD, Villenave R, Yadid M, Parker KK, Ingber DE.

* Fluidic and microfluidic tools for quantitative systems biology. Okumus B, Yildiz S, Toprak E. Curr Opin Biotechnol. 2014 Feb;25:30-8. doi: 10.1016/j.copbio.2013.08.016. Epub 2013 Sep 14

* Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation. Uphoff S, Lord ND, Okumus B, Potvin-Trottier L, Sherratt DJ, Paulsson J. Science. 2016 Mar 4;351(6277):1094-7. doi: 10.1126/science.aac9786.

* Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Okumus B, Landgraf D, Lai GC, Bakhsi S, Arias-Castro JC, Yildiz S, Huh D, Fernandez-Lopez R, Peterson CN, Toprak E, El Karoui M, Paulsson J. Nat Commun. 2016 May 18;7:11641. doi: 10.1038/ncomms11641.

* Corrigendum: Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Okumus B, Landgraf D, Lai GC, Bakshi S, Arias-Castro JC, Yildiz S, Huh D, Fernandez-Lopez R, Peterson CN, Toprak E, El Karoui M, Paulsson J. Nat Commun. 2016 Jun 24;7:12130. doi: 10.1038/ncomms12130

​* Design of a Microfluidic Chip for Magnetic-Activated Sorting of One-Bead-One-Compound Libraries. Cho CF, Lee K, Speranza MC, Bononi FC, Viapiano MS, Luyt LG, Weissleder R, Chiocca EA, Lee H, Lawler SE. ACS Comb Sci. 2016 Jun 13;18(6):271-8. doi: 10.1021/acscombsci.5b00180

* Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling. Estrada J, Andrew N, Gibson D, Chang F, Gnad F, Gunawardena J.

* Distinct kinetic and mechanical properties govern mucin 16- and podocalyxin-mediated tumor cell adhesion to E- and L-selectin in shear flow. Shea DJ, Wirtz D, Stebe KJ, Konstantopoulos K.

* Interplay of the physical microenvironment, contact guidance, and intracellular signaling in cell decision making. Paul CD, Shea DJ, Mahoney MR, Chai A, Laney V, Hung WC, Konstantopoulos K.

* Optimization of Pathogen Capture in Flowing Fluids with Magnetic Nanoparticles. Kang JH, Um E, Diaz A, Driscoll H, Rodas MJ, Domansky K, Watters AL, Super M, Stone HA, Ingber DE.

* On-chip immobilization of planarians for in vivo imaging. Dexter JP, Tamme MB, Lind CH, Collins EM.

* Synchronous long-term oscillations in a synthetic gene circuit. Potvin-Trottier L, Lord ND, Vinnicombe G, Paulsson J.

* Membrane dynamics of dividing cells imaged by lattice light-sheet microscopy. Aguet F, Upadhyayula S, Gaudin R, Chou YY, Cocucci E, He K, Chen BC, Mosaliganti K, Pasham M, Skillern W, Legant WR, Liu TL, Findlay G, Marino E, Danuser G, Megason S, Betzig E, Kirchhausen T.

* Accurate concentration control of mitochondria and nucleoids. Jajoo R, Jung Y, Huh D, Viana MP, Rafelski SM, Springer M, Paulsson J. Science. 2016 Jan 8;351(6269):169-72. doi: 10.1126/science.aaa8714.