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:

  • Cell-free reconstitution of peroxisomal matrix protein import using Xenopus egg extract. Michael L. Skowyra1,2,∗ and Tom A. Rapoport1,3,∗∗ STAR Protoc. 2023 Feb 10; 4(1):102111. PMID: 36853666; PMCID: PMC9947420.
  • HIV silencing and cell survival signatures in infected T cell reservoirs. Iain C. Clark, Prakriti Mudvari, Shravan Thaploo, Samuel Smith, Mohammad Abu-Laban, Mehdi Hamouda, Marc Theberge, Sakshi Shah, Sung Hee Ko, Liliana Pérez, Daniel G. Bunis, James S. Lee, Divya Kilam, Saami Zakaria, Sally Choi, Samuel Darko, Amy R. Henry, Michael A. Wheeler, Rebecca Hoh, Salwan Butrus, Steven G. Deeks, Francisco J. Quintana, Daniel C. Douek, Adam R. Abate & Eli A. Boritz . Nature volume 614, pages318–325 (2023)
  • Cell wall synthesis and remodeling dynamics determine division site architecture and cell shape in Escherichia coli Paula P. Navarro, Andrea Vettiger, Virly Y. Ananda, Paula Montero Llopis, Christoph Allolio, Thomas G. Bernhardt & Luke H. Chao. Nature Microbiology volume 7, pages1621–1634 (2022)
  • A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors. Dorothy Koveal, Paul C Rosen, Dylan J Meyer, Carlos Manlio Díaz-García, Yongcheng Wang, Li-Heng Cai, Peter J Chou, David A Weitz, and Gary Yellen. 2022. Nat Commun, 13, 1, Pp. 2919. Published online 2022 May 25. doi: 10.1038/s41467-022-30685-x. PMCID: PMC9133083 PMID: 35614105.
  • Vinculin plays a role in neutrophil stiffening and transit through model capillary segments. Brittany M. Neumann, Zachary S. Wilson, Kinga Auguste, Yasmin Roye, Manisha K. Shah, Eric M. Darling, Craig T. Lefort. doi: https://doi.org/10.1101/2022.04.24.489286
  • A role for the Gram-negative outer membrane in bacterial shape determination. Elayne M Fivenson, Patricia D A Rohs, Andrea Vettiger, Marios F Sardis, Grasiela Torres, Alison Forchoh, Thomas G Bernhardt PMID: 36778245 PMCID: PMC9915748 DOI: 10.1101/2023.02.03.527047
  • PIEZO1 mediates a mechanothrombotic pathway in diabetes. Wandi Zhu, wzhu5@bwh.harvard.edu; Calum A. MacRae, cmacrae@bwh.harvard.edu. SCIENCE TRANSLATIONAL MEDICINE. 5 Jan 2022. Vol 14, Issue 626

    DOI: 10.1126/scitranslmed.abk1707. Link here

  • Barcoded viral tracing of single-cell interactions in central nervous system inflammation. Iain C. Clark, Cristina Gutiérrez-Vázquez, Michael A. Wheeler, Zhaorong Li, Veit Rothhammer, Mathias Linnerbauer, Liliana M. Sanmarco, Lydia Guo, Manon Blain, Stephanie E. J. Zandee, Chun-Cheih Chao, Katelyn V. Batterman, Marius Schwabenland, Peter Lotfy, Amalia Tejeda-Velarde, Patrick Hewson, Carolina Manganeli Polonio, Michael W. Shultis, Yasmin Salem, Emily C. Tjon, Pedro H. Fonseca-Castro, Davis M. Borucki, Kalil Alves de Lima, Agustin Plasencia, Adam R. Abate, Douglas L. Rosene, Kevin J. Hodgetts, Marco Prinz, Jack P. Antel, Alexandre Prat, and Francisco J. Quintana. SCIENCE 23 Apr 2021 Vol 372, Issue 6540 DOI: 10.1126/science.abf1230.
  • In situ reprogramming of gut bacteria by oral delivery Bryan B. Hsu, Isaac N. Plant, Lorena Lyon, Frances M. Anastassacos, Jeffrey C. Way & Pamela A. Silver. Nature Communications volume 11, Article number: 5030 (2020)
  • Targeted Single-Cell RNA and DNA Sequencing With Fluorescence-Activated Droplet Merger Iain C. Clark, Cyrille L. Delley, Chen Sun, Rohan Thakur, Shannon L. Stott, Shravan Thaploo, Zhaorong Li, Francisco J. Quintana, and Adam R. Abate. Anal. Chem. 2020, 92, 21, 14616–14623 Publication Date:October 13, 2020 https://doi.org/10.1021/acs.analchem.0c03059

  • Manipulation and Sorting of Cell-Laden Hydrogel Microcapsules Within Microfluidic Environment. Dhingra, Karan. 2019 http://hdl.handle.net/10393/39858
    http://dx.doi.org/10.20381/ruor-24097

  • Guided tissue organization and disease modeling in a kidney tubule array. Subramanian B1, Kaya O2, Pollak, Yao G2, Zhou J4. Biomaterials. 2018 Nov;183:295-305. doi: 10.1016/j.biomaterials.2018.07.059. Epub 2018 Aug 10. Link here.
  • Enzymatic DNA synthesis for digital information storage. Henry H. Lee, Reza Kalhor, Naveen Goela, Jean Bolot, George M. Church. bioRxiv 348987; Link here
  • 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. Sci Rep. 2016 Dec 1;6:37949. doi: 10.1038/srep37949, “Laser Speckle Rheology for evaluating the viscoelastic properties of hydrogel scaffolds.” Scientific Reports 6 (1): 37949. doi:10.1038/srep37949. link here
  • 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. Genome Res. 2016 Oct;26(10):1397-1410. Epub 2016 Jul 28. Genome Research, 2016 Oct, Vol.26(10), pp.1397-1410. Link here
  • 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. Cell Syst. 2016 Oct 26;3(4):346-360.e4. doi: 10.1016/j.cels.2016.08.011. Epub 2016 Sep 22. Cell Systems, 26 October 2016, Vol.3(4), pp.346-360.e4. Link here
  • 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 . Link here
  • 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.Annu Rev Pathol. 2015;10:195-262. doi: 10.1146/annurev-pathol-012414-040418. Annual Review of Pathology: Mechanisms of Disease, 2015, Vol.10, p.195-262. Link here
  • Fluidic and microfluidic tools for quantitative systems biology. Okumus B, Yildiz S, Toprak E. Curr Opin Biotechnol. Curr Opin Biotechnol. 2014 Feb;25:30-8. doi: 10.1016/j.copbio.2013.08.016. Epub 2013 Sep 14. Current Opinion in Biotechnology, February 2014, Vol.25, pp.30-38. Link here
  • 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. Life Science Weekly, March 29, 2016, p.551. Link here
  • 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. Nat Commun. 2016 Jun 24;7:12130. doi: 10.1038/ncomms12130.Nature Communications, 2016, Vol.7 . Link here
  • 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. Nat Commun. 2016 Jun 24;7:12130. doi: 10.1038/ncomms12130. Nature Communications, 2016, Vol.7. Link here
  • ​ 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. ACS Comb Sci. 2016 Jun 13;18(6):271-8. doi: 10.1021/acscombsci.5b00180. Epub 2016 May 23. ACS combinatorial science, 13 June 2016, Vol.18(6), pp.271-8. Link here
  • 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. PLoS Comput Biol. 2016 Jul 1;12(7):e1004995. doi: 10.1371/journal.pcbi.1004995. eCollection 2016 Jul. Estrada, Javier, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad, and Jeremy Gunawardena. 2016. “Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.” PLoS Computational Biology 12 (7): e1004995. doi:10.1371/journal.pcbi.1004995. Link here
  • 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. Oncotarget. 2015 Sep 22;6(28):24842-55. doi: 10.18632/oncotarget.4704. Oncotarget, 2015 Sep 22, Vol.6(28), pp.24842-24855. Link here
  • 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.FASEB J. 2016 Jun;30(6):2161-70. doi: 10.1096/fj.201500199R. Epub 2016 Feb 22. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, June 2016, Vol.30(6), pp.2161-70. Link here
  • 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.Small. 2015 Nov 11;11(42):5657-66. doi: 10.1002/smll.201501820. Epub 2015 Sep 21.Small, November 2015, Vol.11(42), pp.5657-5666. Link here
  • On-chip immobilization of planarians for in vivo imaging. Dexter JP, Tamme MB, Lind CH, Collins EM. Sci Rep. 2014 Sep 17;4:6388. doi: 10.1038/srep06388. Scientific Reports, 2014, Vol.4. Link here
  • Synchronous long-term oscillations in a synthetic gene circuit. Potvin-Trottier, Laurent, Nathan D. Lord, Glenn Vinnicombe, and Johan Paulsson. 2017. “Synchronous long-term oscillations in a synthetic gene circuit.” Nature 538 (7626): 514-517. doi:10.1038/nature19841. http://dx.doi.org/10.1038/nature19841 . Link here
  • 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.Mol Biol Cell. 2016 Nov 7;27(22):3418-3435. Epub 2016 Aug 17.Molecular biology of the cell, 07 November 2016, Vol.27(22), pp.3418-3435. Link here
  • 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. Science (New York, N.Y.), 08 January 2016,Vol.351(6269), pp.169-72. Link here
  • Single-cell barcoding and sequencing using droplet microfluidics. Zilionis R, Nainys J, Veres A Savova V, Zemmour D, Klein AM, Mazutis L. Jan;12(1):44-73. Epub 2016 Dec 8. doi: 10.1038/nprot.2016.154 Link here.
  • Sequential conformational rearrangements in flavivirus membrane fusion. Luke H Chao, Daryl E Klein, Aaron G Schmidt, Jennifer M Peña, Stephen C Harrison. Structural Biology and Molecular Biophysics. eLife 2014;3:e04389 DOI: 10.7554/eLife.04389
  • 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. Epub 2013 Aug 21. Journal of Virology, 2013, Vol. 87(21), p.11637. Link here
  • Memory and Modularity in Cell-Fate Decision Making. Thomas M. Norman, Nathan D. lord, Johan Paulsson,Richard Losick. Nature. 2013 Nov 28;503(7477):481-486. doi: 10.1038/nature12804. Epub 2013 Nov 20. Link here
  • 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. Analyst. 2014 Jul 7;139(13):3235-44. doi: 10.1039/c4an00091a. The Analyst, 2014, Vol.139(13), pp.3235-3244. Link here.
  • 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.Nat Methods. 2014 Jun;11(6):663-9. doi: 10.1038/nmeth.2938. Epub 2014 May 4. Nature Methods, June, 2014, Vol.11(6), p.663(9). Link here.
  • Microengineered physiological biomimicry: Organs-on-Chips. Dongeun Huh, Yu-suke Torisawa, Geraldine A. Hamilton, Hyun Jung Kima and Donald E. Ingber. Lab Chip. 2012 Jun 21;12(12):2156-64. doi: 10.1039/c2lc40089h. Epub 2012 May 3. Lab on a Chip, 2012, Vol.12(12), pp.2156-2164. Link here.
  • ​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. Integr Biol (Camb). Integr Biol (Camb). 2013 Feb;5(2):381-9. doi: 10.1039/c2ib20209c. Integrative Biology, 2013, Vol.5(2), pp.381-389. Link here.
  • 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. Nat Med. 2014 Oct;20(10):1211-6. doi: 10.1038/nm.3640. Epub 2014 Sep 14. Nature Medicine, 2014. Link here.
  • 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. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4869-77. doi: 10.1073/pnas.1403438111. Epub 2014 Oct 27. Proc. Natl. Acad. Sci. USA, 2015, Vol.111(45). Link here.
  • 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.Cancer Discov. 2014 Apr;4(4):452-65. doi: 10.1158/2159-8290.CD-13-0646. Epub 2014 Jan 20. Cancer discovery, April 2014, Vol.4(4), pp.452-65. Link here.
  • 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.Integr Biol (Camb). 2013 Dec;5(12):1474-84. doi: 10.1039/c3ib40082d.ntegrative Biology, 2013, Vol.5(12), pp.1474-1484. Link here.
  • 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. Cell. 2015 May 21;161(5):1187-1201. doi: 10.1016/j.cell.2015.04.044. Cell, 21 May 2015, Vol.161(5), pp.1187-1201. Link here.
  • 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. Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. Cell, 21 May 2015, Vol.161(5), pp.1202-1214. Link here.