Representative publications featuring FlowJEM's products and services:

1. Wheeler, J.H.R., Foster, K.R., Durham, W. M.  (2024) Individual bacterial cells can use spatial sensing of chemical gradients to direct chemotaxis on surfaces. Nature Microbiology 9, 2308–2322. doi: org/10.1038/s41564-024-01729-3
2. Orzolek, L.D. (2024) Sequencing: 10X Genomics 3′ HT Assay for Gene Expression. In RNA Amplification and Analysis: Methods and Protocols. New York, NY: Springer US, 207-226.   doi: org/10.1007/978-1-0716-3918-4_15 
3. Jarzebska, N.T., Frei, J., Mellett, M., Kündig, T.M., Steve Pascolo, S., Reichmuth, A. M. (2024) A basic method for formulating mRNA-lipid nanoparticle vaccines in the lab. RNA Vaccines ​Methods and Protocols (book), 237–254 doi: org/10.1007/978-1-0716-3770-8_11
4. Mitchell Josvai. M., Polyak, E., Kalluri, M., Robertson, S., Crone, W.C., Suzuki, M. (2024) An engineered in vitro model of the human myotendinous junction. Acta Biomaterialia 180, 279-294. doi: org/10.1016/j.actbio.2024.04.007
5. Fishman, L., Modak, A., Nechooshtan, G., Razin, T., Erhard, F., Regev, A., Farrell, J.A., Rabani, M. (2024) Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nature Commun. 15, Article number: 3104. doi: org/10.1038/s41467-024-47290-9
6. Feulner, L., Wünnemann, F., … Piet van Vliet, P., Andelfinge, G. (2024) Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution. bioRxiv doi: org/10.1101/2024.03.05.583423.
7. Florini, F., Visone, J.E., Hadjimichael, E., Malpotra, S., Nötzel, C., Kafsack, B.F.C., Deitsch, K.W. (2024) Transcriptional plasticity of virulence genes provides malaria parasites with greater adaptive capacity for avoiding host immunity. bioRxiv doi: org/10.1101/2024.03.08.584127
8. Yakavets, I., Ayachit, M., Kheiri, S., Chen, Z., Rakhshani, F., McWhirter, S., Young, E.W.K., C. Walker, G.C., Kumacheva, E. (2024) A microfluidic platform for evaluating the internalization of liposome drug carriers in tumor spheroids. ACS Applied Materials & Interfaces 16 (8), 9690–9701. doi: org/10.1021/acsami.3c16330
9. Wheeler, J.H.R., Foster, K. R., Durham, W. M. (2024) Bacteria use spatial sensing to direct chemotaxis on surfaces. bioRxiv , doi: org/10.1101/2024.02.13.580113
10. Li, R.G., Li, X., … Samee, M.A.H., Martin, J. F. (2024) YAP induces a neonatal-like pro-renewal niche in the adult heart. Nature Cardiovascular Research 3, 283–300. doi: org/10.1038/s44161-024-00428-w
11. Zhao, J., Zarabadi, M., Hall, D., Dahal, S., Greener, J., Yang, L.  (2024) Unification of cell-scale metabolic activity with biofilm behavior by integration of advanced flow and reactive-transport modeling and microfluidic experiments. bioRxiv doi: org/10.1101/2024.01.25.577134
12. Garcia-Bonilla, L., Shahanoor, Z., Sciortino, R.,  Nazarzoda, O., Racchumi, G., Iadecola, C., Anrather, J. (2024) Analysis of brain and blood single-cell transcriptomics in acute and subacute phases after experimental stroke. Nature Immunology 25, 357–370. doi: org/10.1038/s41590-023-01711-x
13. Long, H., Steimle, J.D., …Samee, M.A.H., Martin, J.F. (2024) Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury. Life Science Alliance 7(2) e202201870. doi: org/10.26508/lsa.202201870 
14. Stempien, A., Josvai, M., Notbohm, J., Zhang, J., Kamp, T. J., Crone, W. C. (2024) Influence of remodeled ECM and co-culture with iPSC-derived cardiac fibroblasts on the mechanical function of micropatterned iPSC-derived cardiomyocytes. Cardiovascular Engineering and Technol. 15, 264–278. Doi: org/10.1007/s13239-024-00711-8
15. Malawsky, D.S., Dismuke,T, Liu,H., Castellino, E., Brenman, J., Dasgupta, B., Tikunov, A., Gershon, T.R.1 (2023) Chronic AMPK inactivation slows SHH medulloblastoma progression by inhibiting mTORC1 signaling and depleting tumor stem cells. iScience 26, 108443. doi: org/10.1016/j.isci2023.1084443
16. Zhang, L., Parvin, R., Chen, M., Hu, D., Fan, Q., Ye, F. (2023) High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosensors and Bioelectronics. 228, 115213. doi: org/10.1016/j.bios.2023.115213
17. Babcock, B., Seth Weir, S. (2023) scRNA-seq for Microcephaly Research [I]: Single-cell droplet encapsulation, mRNA capture, and cDNA synthesis.  Microcephaly.  Protocol 83–97.  doi: 10.1007/978-1-0716-2752-5_8
18. Gerayeli, F.V., Stephen Milne, S., … Leung, J.M., Sin, D.D. (2023) Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol. bioRxiv. doi: org/10.1101/2023.03.02.530288
19. De Lange, W. J., Farrell, E. T. … Crone, W. C., Ralphe, J. C. (2023) cMyBP-C-ablation-in-human-engineered-cardiacineered cardiac tissue causes progressive Ca2+-handling abnormalities. J Gen Physiol. 155 (4): e202213204.
20. Arrigoni, C., Ostano, P., … Chiorino, G., Moretti, M. (2023) Differential angiogenesis of bone and muscle endothelium in aging and inflammatory processes. Communications Biology 6, Article number 126.
21. Hong, J., Wong, B., Huynh, C., Tang, B., Umar, S., Yang, X., Eghbali, M. (2023) A Tm4sf1-marked subpopulation of endothelial stem/progenitor cells identified by lung single-cell omics of pulmonary arterial hypertension. Am. J. Respir. Cell Mol. Biol.  68(4):381-394.
22. Orbach, S.M., Brooks, M. D. … Jeruss, J. S., Shea, L. D. (2022) Single-cell RNA-sequencing identifies anti-cancer immune phenotypes in the early lung metastatic niche during breast cancer. Clin Exp Metastasis 39, 865–881.
23. Gong, L., Khodaparastasgarabad, N., Hall, D. M., Greener, J. A new angle to control concentration profiles at electroactive biofilm interfaces: Investigating a microfluidic perpendicular flow approach. (2022) Electrochimica Acta 431, 1, 141071
24. Nötzel, C., Kafsack, B. F. C.  (2022) PfD123 modulates K13-mediated survival and recovery after artemisinin exposure. BioRxiv 
25. Lee, K., Tripathi, A. (2022) An investigation into simplifying total RNA extraction with minimal equipment using a low volume, electrokinetically driven microfluidic protocol. Biomicrofluidics 16, 044107.
26. Ocasio, J., Babcock, B., Malawsky, D., Weir, S.J., Loo, L., Simon, J.M., Mark J. Zylka, M.J., ... & Gershon, T.R. (2022) scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy. Nature Communications 10, Article number 5829.
27. Salmen, F., Jonghe, J., … Florian Hollfelder, F., Oudenaarden, A. (2022) High-throughput total RNA sequencing in single cells using VASA-seq. Nature Biotechnology  
28. ​Bonneuil, W. V., Watson, D. J., Frattolin, J., Russell, M. J., Masci, F. F., Bandara, M., Brook, B. S., Nibbs, R. J. B.,  Moore, J. E. (2022) Generation of Stable Advective-Diffusive Chemokine Gradients in a Three-Dimensional Hydrogel. AIP Advances 12, 025121 
29. Nötzel, C., Kafsack, B. F. C. (2022) Pfd123 Modulates K13-Mediated Survival and Recovery after Artemisinin Exposure. BioRxiv  
30. Prince, E., Kheiri, S., Wang, Y., Xu, F., Cruickshank, J., … Cescon, D. W., Kumacheva, E. (2021) Microfluidic Arrays of Breast Tumor Spheroids for Drug Screening and Personalized Cancer Therapies. Adv. Healthcare. Materials 11, 2101085
31. Pham, V. M., Ha, H. T.T., Thakor, N. (2021) Microfluidic culture platforms in neuroscience research. In Handbook of Neuroengineering, Springer Reference, pp 1-39.
32. Garcia-Agudo, L.F, Steixner-Kumar, A.A., Curto, Y., Nacher, J., Nave, K.-A., Ehrenreich, H.  (2021) Brain erythropoietin fine-tunes a counterbalance between neurodifferentiation and microglia in the adult hippocampus. Cell Reports 36, 109548. 
33. Araki, D., Fu, J. F., ... Larochelle, A. (2021) NOTCH-mediated ex vivo expansion of human hematopoietic stem and progenitor cells by culture under hypoxia. Stem Cell Reports 16(9):2336-2350.​
34. Carraro, G., Langerman, J., …, Gomperts, B.N. (2021) Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition. Nature Medicine 27, 806–814.
35. Huang, W.-K., Wong, S. Z. H., Pather, S. R., … Ming. G.-li. (2021) Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells. Cell Stem Cell 28(9),1657-1670.e10.​
36. Schneider, L., Cui, F., Tripathia, A.* (2021) Isolation of target DNA using synergistic magnetic bead transport and electrokinetic flow. Biomicrofluidics 15, 024104. 
37. Zhang, Z., Park, J. W., Ahn, I. S., Diamante, G., Sivakumar, N., Arneson, D., Yang, X., van Veen, E, J., Correa, S. M. (2021) Estrogen receptor alpha in the brain mediates tamoxifen-induced changes in physiology in mice. eLife 2021;10:e63333.
38. Saikia, M., Holter, M. M., Donahue, L. R., … Cummings, B. P. (2021) GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells. JCI Insight 6(3):e141851. 
39. Park, S.R., Namkoong, S.,  Friesen. L., … ,  Lee, J. H. (2020) Single-cell transcriptome analysis of colon cancer cell response to 5-Fluorouracil-induced DNA damage. Cell Reports  32, 8, 108077.
40. Brann, D. H., Tsukahara, T., Lipovsek, M., … Datta, S.R. (2020) Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances, eabc5801. 
41. Deraney, R. N., Schneider, L., Tripathi, A. (2020) Synergistic use of electroosmotic flow and magnetic forces for nucleic acid extraction. Analyst 145, 2412-2419.
42. Jacob, F., Salinas, R.D., Zhang, D.Y., Nguyen, P.T.T., Schnoll, J.G., ...& Song, H. (2020) ​A patient-derived glioblastoma organoid model and biobank recapitulates inter- and intra-tumoral heterogeneity. Cell 180, 188-204. e22.
43. Wakhloo, D., Scharkowski, F., Curto, Y., Butt, U.J., Bansal, V., Klaus-Armin Nave, K-A.,... & Ehrenreich, H. (2020) Functional hypoxia drives neuroplasticity and neurogenesis via brain erythropoietin. Nature Communications 11, Article number: 1313.
44. Tran, R., Lam, W.A. (2019). Microfluidic approach for highly efficient viral transduction. In Methods in Molecular Biology (MIMB, 2097). Cell Reprogramming for Immunotherapy, pp. 55-65.
45. Luo, F., Guo, L., Zhang, Q., Ling, Y., Yang, Z., Grigoriev, S.A., Cheng, H. (2019). Boosting CO tolerance and stability of Pt electrocatalyst supported on sulfonated carbon nanotubes. International Journal of Hydrogen Energy 44, 29671-29679.
46. Zarabadi, M. P., Couture, M., Charette, S. J., Greener, J. (2019) Generalized kinetic framework applied to whole-cell bioelectrocatalysis in bioflow reactors clarifies performance enhancements for Geobacter Sulfurreducens biofilms. ChemElectroChem 6, 10, 2715-2718
47. Gryder, B.E., Pomella, S., Sayers, C., Wu, X.S., Song, Y., Chiarella, A.M., ... & Khan, J. (2019) Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nature Genetics 51, 1714–1722.
48. Francesko, A., Vanessa F. Cardoso, V. F., Lanceros-Méndez, S.L. (2019). In Microfluidics for Pharmaceutical Applications. Lab-on-a-chip technology and microfluidics, pp. 3-36.
49. Sonnen, K.F., Christoph A.Merten, C.A. (2019). Microfluidics as an emerging precision tool in developmental biology. Developmental Cell 48, 293-311.
50. Kang, B., Alvarado, L.J., Kim, T., Lehmann, M.L., Cho, H., He, J., Li, P., Kim, B-H., Larochelle, A., ... & Kelsall, B.L. (2019). Commensal microbiota drive the functional diversification of colon macrophages. Mucosal Immunology, 1–14. DOI: 10.1038/s41385-019-0228-3.
51. Rajbhandari, P., Arneson, D., Hart, S.K., Ahn, I.S., Diamante, G., Santos, L.C., Zaghari, N.,...& Tontonoz, P. (2019) Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes. eLife 8: e49501. DOI: .10.7554/eLife.4950.
52. Bhetraratana, M., Orozco, L.D., Hong, J., Diamante, G., Majid, S.,...& Araujo, A. (2019). Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies. Archives of Biochemistry and Biophysics 678, 108116.
53. Sheth, R.U., Li, M., Jiang, W., Sims, P.A., Leong, K.W   & Wang, H,H. (2019) Spatial metagenomic characterization of microbial biogeography in the gut. Nature Biotechnology 37, 877–883
54. Notbohm, J., Napiwocki, B.N., de Lange, W.J., ... & Crone, W.C. (2019) Two-dimensional culture systems to enable mechanics-based assays for stem cell-derived cardiomyocytes. Experimental Mechanics 59, 1235–1248.
55. Saikia, M., Burnham, P., Keshavjee, S.H., Wang, M.F.Z., Heyang, M., ...& De Vlaminck, I. (2019) Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nature Methods 16, 59–62
56. Zarabadi, M. P., Charette, S. J., Greener, J. (2018) Flow-Based deacidification of Geobacter sulfurreducens biofilms depends on nutrient conditions: a microfluidic bioelectrochemical study. ChemElectroChem 5, 23, 3645-3653. 
57. Plass, M., Solana, J., Wolf, F.A., Ayoub, S., Misios, A., Glažar, P., Obermayer, B., Theis, F.J., Kocks, C., Rajewsky, N. (2018) Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science. 360,  Issue 6391, eaaq1723. 
58. Arneson, D., Zhang, G., Ying, Z., Zhuang, Y., Byun, H. R., Ahn, I. S., ... & Yang, X. (2018) Single cell molecular alterations reveal target cells and pathways of concussive brain injury. Nature Communications, 9, Article number 3894.
59. Xiao, Y., Hill, M.C., Zhang, M., Martin, T. J., Morikawa, Y., Wang, S., ... & Martin, J. F. (2018) Hippo signaling plays an essential role in cell state transitions during cardiac fibroblast development. Developmental Cell 45, 153-169.
60. Seah, Y. F. S., Hu, H., & Merten, C. A. (2018) Microfluidic single-cell technology in immunology and antibody screening. Molecular Aspects of Medicine 59, 47-61.
61. Poustia, M., Greener, J. (2018) Altered biofilm formation at plasma bonded surfaces in microchannels studied by attenuated total reflection infrared spectroscopy. Surface Science 676, 56-60.
62. Bageritz, J., Raddi, G. (2018) Single-cell RNA sequencing with drop-seq. Single Cell Methods   1979, 73-85.
63. Schmidt, G.W., Frey, O., Rudolf, F. (2018) The cellclamper: a convenient microfluidic device for time-lapse imaging of yeast. Genome Instability 1672, 537-555.
64. Carboni, E.J., Bognet, B.H., Cowles, D.B., Ma, A.W.K. (2018) The margination of particles in areas of constricted blood flow. Biophysical Journal 114, 9, 2221-2230.
65. Wu, H., Uchimura, K., Donnelly, E.L., Kirita, Y., Morris, S.A., Humphreys, B.D. (2018) Comparative analysis and refinement of human PSC-derived kidney organoid differentiation with single-cell transcriptomics. Cell Stem Cell 23, 869-881.e8.
66. Zywitza, V., Misios, A., Bunatyan, L., Willnow, T.E., Rajewsky, N. (2018) Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis. Cell Reports 25, 2457-2469.e8.
67. Scavuzzo, M.A, Hill, M.C., Chmielowiec, J., Yang, D., Teaw, J., Sheng, K., Kong, Y., ... & Borowiak M. (2018). Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. Nature Communications. 9, Article number: 3356.
68. Walsh III, D. I., Kong, D. S., Murthy, S. K., & Carr, P. A. (2017). Enabling microfluidics: from clean rooms to makerspaces. Trends in Biotechnology 35, 383-392.
69. Karaiskos, N., Wahle, P., Alles, J., Boltengagen, A., Ayoub, S., Kipar, C., ... & Zinzen, R. P. (2017). The Drosophila embryo at single-cell transcriptome resolution. Science 358, 194-199.
70. Romanov, R. A., Zeisel, A., Bakker, J., Girach, F., Hellysaz, A., Tomer, R., ... & Hsueh, B. (2017) Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nature Neuroscience 20, 176–188.
71. Datlinger, P., Rendeiro, A. F., Schmidl, C., Krausgruber, T., Traxler, P., Klughammer, J., ... & Bock, C. (2017) Pooled CRISPR screening with single-cell transcriptome readout. Nature Methods 14, 297.
72. Gierahn, T. M., Wadsworth II, M. H., Hughes, T. K., Bryson, B. D., Butler, A., Satija, R., ... & Shalek, A. K. (2017) Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nature Methods 14, 395.
73. Poran, A., Nötzel, C., Aly, O., Mencia-Trinchant, N., Harris, C. T., Guzman, M. L., ... & Kafsack, B. F. (2017) Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites. Nature 551, 95-99.
74. Alles, J., Karaiskos, N., Praktiknjo, S. D., Grosswendt, S., Wahle, P., Ruffault, P. L., ... & Zinzen, R. (2017) Cell fixation and preservation for droplet-based single-cell transcriptomics. BMC Biology 15, Article number 44.
75. Miled, A., Greener, J. (2017) Recent advancements towards full-system microfluidics. Sensors 17, 1707.
76. Huang,H., Singh, K., Hart, A.C. (2017) Measuring Caenorhabditis elegans sleep during the transition to adulthood using a microfluidics-based system. Bio Protoc. 7, e2174. DOI: 10.21769/BioProtoc.2174.
77. Zarabadi, M.P., Paquet-Mercier, F., Charette, S.J., Greener, J. (2017) Hydrodynamic effects on biofilms at the biointerface using a microfluidic electrochemical cell: case study of pseudomonas sp. Langmuir 33, 2041-2049
78. Ware, B.R., Khetani, S.R. (2017). In Edge-Detection for Contractility Measurements with Cardiac Spheroids", M. Clements, L. Roquemore (Eds.) Stem Cell-Derived Models in Toxicology Series. Micropatterned co-cultures of induced pluripotent stem cell-derived hepatocytes and stromal cells for drug toxicity studies, pp. 311-334.
79. Greener, J.; Gashti, M. P., Eslami, A., Zarabadi, M. P., Taghavi, S. M. (2016) A microfluidic method and custom model for continuous, non-intrusive biofilm viscosity measurements under different nutrient conditions. Biomicrofluidics 10, 064107.  
80. Debono, M., Voicu, D., Pousti, M., Safdar, M.,Young, R., Kumacheva, E., Greener, J. (2016) One-step fabrication of microchannels with integrated three-dimensional features by hot intrusion embossing. Sensors 16, 2023.
81. Kara, A., Mathault, J., Reitz, A., Boisvert, M., Tessier, F., Greener, J., Miled, A. (2016) Microfluidic in-channel multi-electrode platform for neurotransmitter sensing. SPIE Proceedings vol. 9705: Microfluidics, BioMEMS, and Medical Microsystems XIV.
82. Nayak, S., Blumenfeld, N. R., Laksanasopin, T., Sia, S. K. (2016). Point-of-care diagnostics: recent developments in a connected age. Analytical Chemistry 89, 102-123.
83. Yuan, J., & Sims, P. A. (2016) An automated microwell platform for large-scale single cell RNA-Seq. Scientific Reports 6, 33883
84. Oliveira, N. M., Foster, K. R., & Durham, W. M. (2016) Single-cell twitching chemotaxis in developing biofilms. Proceedings of the National Academy of Sciences 113, 6532-6537.
85. Gashti, M. P., Asselin, J., Barbeau, J., Boudreau, D., & Greener, J. (2016) A microfluidic platform with pH imaging for chemical and hydrodynamic stimulation of intact oral biofilms. Lab on a Chip, 16, 1412-1419
86. Paquet-Mercier, F., Gashti, M. P., Bellavance, J., Taghavi, S. M., & Greener, J. (2016) Through thick and thin: a microfluidic a roach for continuous measurements of biofilm viscosity and the effect of ionic strength. Lab on a Chip 16, 4710-4717.
87. Temiz Y., Lovchik RD., Kaigala GV., Delamarche E. (2015) Lab-on-a-chip devices: How to close and plug the lab? Microelectronic Engineering 132, 156-175.
88. March, S., Ramanan, V., Trehan, K., Ng, S., Galstian, A., Gural, N., & Khetani, S. R. (2015) Micropatterned coculture of primary human hepatocytes and supportive cells for the study of hepatotropic pathogens. Nature Protocols 10, 2027.
89. Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., ... & Trombetta, J. J. (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214.
90. Halldorsson, S., Lucumi, E., Gómez-Sjöbergb, R., Fleming, Ronan M.T. (2015) Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices. Biosensors and Bioelectronics 63, 218-231.
91. Kellogg, R. A., Gómez-Sjöberg, R., Leyrat, A. A., & Tay, S. (2014) High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics. Nature Protocols 9, 1713.
92. Voicu, D., Scholl, C., Li, W., Jagadeesan, D., Nasimova, I., Greener., J., & Kumacheva, E. (2012) Kinetics of multicomponent polymerization reaction studied in a microfluidic format. Macromolecules 45, 4469-4475.
93. Greener, J., Tumarkin, E., Debono, M., Dicks, A. P., & Kumacheva, E. (2012) Education: a microfluidic platform for university-level analytical chemistry laboratories. Lab on a Chip 12, 696-701.