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. 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. http://dx.doi.org/10.1038/srep37949, https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=%E2%...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Upta...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Memo....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Abso...

 

* 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). https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Bone....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Micr...

 

​*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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Scre....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/25216635

 

* 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). https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/25349422

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Inhi....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Comp....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Drop...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=High....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=End+...(ESAT)+expands+the+extractable+information+from+single-cell+RNA-seq+data

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=A+Si....

 

* 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. https://hollis.harvard.edu/primo-explore/fulldisplay?docid=TN_rscc6lc004...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Engi...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Flui...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Stoc....

 

* 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 . https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/27338979

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Corr...

 

​* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Desi....

 

* 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. http://dx.doi.org/10.1371/journal.pcbi.1004995.

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Dist....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Inte....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Opti...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=On-c....

 

* 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.https://www-ncbi-nlm-nih-gov.ezp-p...

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Memb....

 

* 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. https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/?term=Accu...